Index

A

AbstractDuckDbImportStorage (class in gpf.duckdb_storage.duckdb_import_storage) AbstractDuckDbStorage (class in gpf.duckdb_storage.duckdb_genotype_storage) AbstractRunner (class in gpf.tools.gpf_validation_runner) acgt_gpf() (in module gpf.testing.acgt_import) adapt() (gpf.query_variants.query_runners.QueryRunner method) add_argparser_arguments() (gpf.genotype_storage.genotype_storage_genomic_context_cli.CLIGenotypeStorageContextProvider method) (gpf.gpf_instance_plugin.gpf_instance_context_plugin.GPFInstanceContextProvider method) add_arguments() (gpf.gpf_instance.adjustments.adjust_duckdb_storage.AdjustDuckDbStorageCommand static method) (gpf.gpf_instance.adjustments.adjust_impala_storage.AdjustImpalaStorageCommand static method) (users_api.management.commands.user_set_name.Command method) (users_api.management.commands.user_setpasswd.Command method) (users_api.management.commands.users_remove.Command method) add_gene() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) add_measure_task() (gpf.pheno.prepare_data.PreparePhenoBrowserBase method) add_members() (gpf.pedigrees.family.Family method) add_missing_members() (gpf.pedigrees.pedigrees.FamilyConnections static method) add_missing_parquet_fields() (in module gpf.parquet.parquet_writer) add_page() (gpf.pedigrees.drawing.PDFLayoutDrawer method) add_parent() (gpf.studies.study.GenotypeData method) add_pheno_common_inference() (in module gpf.pheno.pheno_import) add_rank() (gpf.pedigrees.pedigrees.Individual method) add_ranks() (gpf.pedigrees.pedigrees.FamilyConnections method) add_tagger() (gpf.pedigrees.family_tag_builder.FamilyTagsBuilder method) add_to_parser() (gpf.variants_loaders.raw.loader.CLIArgument method) add_unnest_in_join() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method) (gpf.query_variants.sql.schema2.base_query_builder.Dialect static method) add_variant_count() (in module gpf.gene_profile.generate_gene_profile) adjust_chrom_prefix() (in module gpf.variants_loaders.raw.flexible_variant_loader) adjust_dataset() (gpf.gpf_instance.adjustments.gpf_instance_adjustments.EnableDisableStudies method) (gpf.gpf_instance.adjustments.gpf_instance_adjustments.StudyConfigsAdjustmentCommand method) adjust_study() (gpf.gpf_instance.adjustments.gpf_instance_adjustments.DefaultGenotypeStorage method) (gpf.gpf_instance.adjustments.gpf_instance_adjustments.EnableDisableStudies method) (gpf.gpf_instance.adjustments.gpf_instance_adjustments.StudyConfigsAdjustmentCommand method) AdjustDuckDbStorageCommand (class in gpf.gpf_instance.adjustments.adjust_duckdb_storage) AdjustImpalaStorageCommand (class in gpf.gpf_instance.adjustments.adjust_impala_storage) AdjustmentsCommand (class in gpf.gpf_instance.adjustments.adjust_command) affected (gpf.variants.attributes.Status attribute) AFFECTED_DAD (gpf.pedigrees.family.FamilyTag attribute) AFFECTED_MOM (gpf.pedigrees.family.FamilyTag attribute) AFFECTED_PRB (gpf.pedigrees.family.FamilyTag attribute) AFFECTED_SIB (gpf.pedigrees.family.FamilyTag attribute) affected_statues (gpf.studies.study.PSCQueryAdjustments attribute) aliases() (gpf.variants.attributes.Sex static method) align_na_results() (gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapter static method) (pheno_tool_api.adapter.PhenoToolAdapter static method) all (gpf.enrichment_tool.event_counters.EnrichmentResult attribute) (gpf.enrichment_tool.event_counters.EventCountersResult attribute) (gpf.enrichment_tool.event_counters.EventsResult attribute) (gpf.enrichment_tool.event_counters.VariantEventsResult attribute) all() (gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method) (gpf.query_variants.attribute_queries.SyntaxSugarTransformer method) all_count() (gpf.pheno.graphs.GraphColumn method) all_labels() (gpf.pedigrees.family.FamilyTag static method) all_region_bins() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) all_tag_labels() (gpf.pedigrees.family.Person method) all_tags() (gpf.pedigrees.family.FamilyTag static method) alla_gpf() (in module gpf.testing.alla_import) Allele (class in gpf.variants.core) Allele.Type (class in gpf.variants.core) allele_count (gpf.variants.family_variant.FamilyVariant property) (gpf.variants.variant.SummaryVariant property) allele_events (gpf.enrichment_tool.genotype_helper.VariantEvent attribute) allele_in_members (gpf.variants.family_variant.FamilyAllele property) allele_in_roles (gpf.variants.family_variant.FamilyAllele property) allele_in_sexes (gpf.variants.family_variant.FamilyAllele property) allele_in_statuses (gpf.variants.family_variant.FamilyAllele property) allele_index (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.variant.SummaryAllele property)

allele_indexes (gpf.variants.family_variant.FamilyVariant property) allele_type (gpf.variants.core.Allele property) (gpf.variants.family_variant.FamilyAllele property) allele_type_from_cshl_variant() (in module gpf.variants.variant) allele_type_from_name() (in module gpf.variants.variant) AlleleEvent (class in gpf.enrichment_tool.genotype_helper) AlleleParquetSerializer (class in gpf.parquet.schema2.serializers) alleles (gpf.variants.family_variant.FamilyVariant property) (gpf.variants.variant.SummaryVariant property) alt_alleles (gpf.variants.variant.SummaryVariant property) alternative (gpf.variants.core.Allele property) (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.variant.SummaryVariant property) and_() (gpf.query_variants.attribute_queries.AttributeQueryTransformerFunction method) (gpf.query_variants.attribute_queries.AttributeQueryTransformerSQL method) (gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method) annotation_schema (gpf.variants_loaders.raw.loader.VariantsLoader property) (gpf.variants_loaders.raw.loader.VariantsLoaderDecorator property) AnnotationPipelineVariantsBatchFilter (class in gpf.parquet.schema2.processing_pipeline) AnnotationPipelineVariantsFilter (class in gpf.parquet.schema2.processing_pipeline) AnnotationPipelineVariantsFilterMixin (class in gpf.parquet.schema2.processing_pipeline) any() (gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method) (gpf.query_variants.attribute_queries.SyntaxSugarTransformer method) append() (gpf.tools.gpf_validation_runner.TestSuite method) append_allele() (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) (gpf.parquet.schema2.variants_parquet_writer.ContinuousParquetFileWriter method) append_meta_to_parquet() (in module gpf.parquet.parquet_writer) apply() (gpf.person_filters.FamilyFilter method) (gpf.person_filters.person_filters.CriteriaFilter method) (gpf.person_filters.person_filters.FamilyFilter method) (gpf.person_filters.person_filters.PersonFilter method) (gpf.person_filters.person_filters.PhenoFilter method) (gpf.person_filters.PersonFilter method) (gpf.person_filters.PhenoFilter method) apply_family_heuristics() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) apply_mask() (gpf.utils.variant_utils.BitmaskEnumTranslator method) apply_summary_heuristics() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) apply_to_df() (gpf.person_filters.FamilyFilter method) (gpf.person_filters.person_filters.FamilyFilter method) (gpf.person_filters.person_filters.PersonFilter method) (gpf.person_filters.person_filters.PersonFilterRange method) (gpf.person_filters.person_filters.PersonFilterSet method) (gpf.person_filters.PersonFilter method) (gpf.person_filters.PersonFilterRange method) (gpf.person_filters.PersonFilterSet method) apply_to_family() (gpf.pedigrees.layout.Layout method) are_mates() (gpf.pedigrees.pedigrees.Individual method) are_siblings() (gpf.pedigrees.pedigrees.Individual method) ARGUMENT (gpf.variants_loaders.raw.loader.ArgumentType attribute) ArgumentType (class in gpf.variants_loaders.raw.loader) array_item_suffix() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method) (gpf.query_variants.sql.schema2.base_query_builder.Dialect static method) AttributeQueriesUnsupportedException AttributeQueryNotSupported AttributeQueryTransformer (class in gpf.query_variants.attribute_queries) AttributeQueryTransformerFunction (class in gpf.query_variants.attribute_queries) AttributeQueryTransformerSQL (class in gpf.query_variants.attribute_queries) AttributeQueryTransformerSQLLegacy (class in gpf.query_variants.attribute_queries) attributes (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.variant.SummaryAllele property) (gpf.variants.variant.SummaryVariant property) authenticate() (utils.authentication.GPFOAuth2Authentication method) (utils.authentication.ReadOnlyDBAuthentication method) (utils.authentication.SessionAuthenticationWithUnauthenticatedCSRF method) autosomal (gpf.variants.attributes.GeneticModel attribute) autosomal_broken (gpf.variants.attributes.GeneticModel attribute)

B

backend (gpf.studies.study.GenotypeDataStudy property) background_id (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground property) (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property) background_type (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground property) (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property) backup_schema2_study() (in module gpf.parquet.schema2.annotate_schema2_parquet) base_dir (gpf.duckdb_storage.duckdb_storage_config.DuckDbConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbParquetConf attribute) (gpf.schema2_storage.schema2_layout.Schema2DatasetLayout attribute) BaseCommonReportsHelper (class in common_reports_api.common_reports_helper) BaseEnrichmentBackground (class in gpf.enrichment_tool.base_enrichment_background) BaseEnrichmentBuilder (class in enrichment_api.enrichment_builder) BaseEnrichmentHelper (class in enrichment_api.enrichment_helper) BaseEnrichmentResourceBackground (class in gpf.enrichment_tool.base_enrichment_background) BaseGenotypeBrowserRunner (class in gpf.tools.gpf_validation_runner) BasePhenoBrowserHelper (class in pheno_browser_api.pheno_browser_helper) BaseQueryBuilder (class in gpf.query_variants.sql.schema2.base_query_builder) BATCH_ROWS (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter attribute) BATCH_SIZE (gpf.schema2_storage.schema2_import_storage.Schema2ImportStorage attribute) best2gt() (in module gpf.utils.variant_utils) best_st (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) best_state (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) bitmask2inheritance() (in module gpf.variants.attributes) BitmaskEnumTranslator (class in gpf.utils.variant_utils) blob_column() (gpf.parquet.schema2.serializers.AlleleParquetSerializer method) (gpf.parquet.schema2.serializers.FamilyAlleleParquetSerializer method) (gpf.parquet.schema2.serializers.SummaryAlleleParquetSerializer method) bold_red (gpf_web.default_settings.CustomFormatter attribute) broken_families (gpf.pedigrees.families_data.FamiliesData property) browsable_figure_path() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method) browser (gpf.pheno.pheno_data.PhenotypeData property) Bucket (class in gpf.import_tools.import_tools) bucket_url (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute) build() (enrichment_api.enrichment_builder.EnrichmentBuilder method) (gpf.gpf_instance.gpf_instance.GPFInstance static method) (gpf.gpf_instance.GPFInstance static method) (gpf.pheno.graphs.GraphColumn static method) (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) build_allele_record_dict() (gpf.parquet.schema2.serializers.AlleleParquetSerializer method) (gpf.parquet.schema2.serializers.FamilyAlleleParquetSerializer method) (gpf.parquet.schema2.serializers.SummaryAlleleParquetSerializer method) build_and_save() (gpf.pheno.pheno_data.PhenotypeData method) (gpf.studies.study.GenotypeData method) build_annotation_filename() (in module gpf.inmemory_storage.annotation_serialization) build_annotation_pipeline() (gpf.import_tools.import_tools.ImportProject method) build_arguments_dict() (gpf.variants_loaders.raw.loader.CLILoader method) (gpf.variants_loaders.raw.loader.VariantsLoaderDecorator method) build_array_join() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect method) (gpf.query_variants.sql.schema2.base_query_builder.Dialect method) build_backend() (gpf.genotype_storage.genotype_storage.GenotypeStorage method) build_batch() (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) build_blob_schema() (gpf.parquet.schema2.serializers.SummaryAlleleParquetSerializer class method) build_cache() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) build_cli_arguments() (gpf.variants_loaders.raw.loader.CLILoader class method) (gpf.variants_loaders.raw.loader.VariantsLoaderDecorator class method) build_cli_arguments_parser() (gpf.tools.liftover_tools.CNVLiftoverTool method) (gpf.tools.liftover_tools.DaeLiftoverTool method) (gpf.tools.liftover_tools.DenovoLiftoverTool method) (gpf.tools.liftover_tools.LiftoverTool method) (gpf.tools.liftover_tools.VCFLiftoverTool method) build_cnv_allele() (gpf.variants.core.Allele static method) build_coding_length_background() (in module gpf.enrichment_tool.build_coding_length_enrichment_background) build_collection() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection static method) (gpf.gene_sets.denovo_gene_set_helpers.DenovoGeneSetHelpers class method) build_config() (gpf.configuration.study_config_builder.StudyConfigBuilder method)

build_configuration() (gpf.gene_profile.db.GeneProfileDBWriter class method) build_enrichment_event_counts_cache() (in module gpf.enrichment_tool.enrichment_cache_builder) build_families_data() (in module gpf.pedigrees.testing) build_families_data_from_pedigree() (gpf.pedigrees.loader.FamiliesLoader static method) build_families_report() (in module gpf.tools.draw_pedigree) build_family() (in module gpf.pedigrees.testing) build_family_layout() (in module gpf.tools.draw_pedigree) build_family_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor method) build_family_schema() (in module gpf.parquet.schema2.serializers) build_family_variants_query() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) build_family_variants_query_runner() (gpf.duckdb_storage.duckdb2_variants.DuckDb2Variants method) (gpf.inmemory_storage.raw_variants.RawFamilyVariants method) (gpf.parquet_storage.storage.ParquetLoaderVariants method) (gpf.query_variants.base_query_variants.QueryVariants method) (gpf.query_variants.sql.schema2.base_variants.SqlSchema2Variants method) build_from_config() (gpf.import_tools.import_tools.ImportProject static method) build_from_file() (gpf.import_tools.import_tools.ImportProject static method) build_gene_regions() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) build_gene_weights_enrichment_background() (in module gpf.enrichment_tool.resource_implementations.enrichment_resource_impl) build_genomic_scores_registry() (gpf.genomic_scores.scores.GenomicScoresRegistry static method) build_genotype_data_all_datasets() (studies.study_wrapper.WDAEStudy static method) build_genotype_data_description() (studies.study_wrapper.WDAEAbstractStudy method) (studies.study_wrapper.WDAEStudy method) build_id() (gpf.pedigrees.family_role_builder.Mating static method) build_import_project() (in module gpf.tools.simple_study_import) build_liftover_pipeline() (gpf.tools.liftover_tools.LiftoverTool method) build_option() (gpf.variants_loaders.raw.loader.CLIArgument method) build_partitions() (in module gpf.gene_profile.generate_gene_profile) build_pheno_browser() (in module gpf.pheno.build_pheno_browser) build_phenotype_study() (gpf.pheno.storage.PhenotypeStorage method) build_position_allele() (gpf.variants.core.Allele static method) build_query() (gpf.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder method) build_rare_query() (in module gpf.gene_profile.generate_gene_profile) build_regression() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method) build_report() (gpf.pheno.pheno_data.PhenotypeData method) (gpf.studies.study.GenotypeData method) build_report_description() (gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapter method) (pheno_tool_api.adapter.PhenoToolAdapter method) build_results() (enrichment_api.enrichment_builder.EnrichmentBuilder method) build_roles() (gpf.pedigrees.family_role_builder.FamilyRoleBuilder method) build_samocha_enrichment_background() (in module gpf.enrichment_tool.resource_implementations.enrichment_resource_impl) build_schema() (gpf.parquet.schema2.serializers.FamilyAlleleParquetSerializer class method) (gpf.parquet.schema2.serializers.SummaryAlleleParquetSerializer class method) (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) build_serializer() (gpf.parquet.schema2.serializers.VariantsDataSerializer static method) build_study_layout() (gpf.duckdb_storage.duckdb_genotype_storage.AbstractDuckDbStorage method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbParquetStorage method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3ParquetStorage method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3Storage method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbStorage method) build_summary_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor method) build_summary_schema() (in module gpf.parquet.schema2.serializers) build_summary_variants_query() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) build_summary_variants_query_runner() (gpf.duckdb_storage.duckdb2_variants.DuckDb2Variants method) (gpf.inmemory_storage.raw_variants.RawFamilyVariants method) (gpf.parquet_storage.storage.ParquetLoaderVariants method) (gpf.query_variants.base_query_variants.QueryVariants method) (gpf.query_variants.sql.schema2.base_variants.SqlSchema2Variants method) build_table() (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) build_table_name() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect method) (gpf.query_variants.sql.schema2.base_query_builder.Dialect method) build_values_categorical_distribution() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method) build_values_ordinal_distribution() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method) build_values_violinplot() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method) build_variant_row() (studies.response_transformer.ResponseTransformer method) (studies.study_wrapper.ResponseTransformerProtocol method) build_variant_types_query() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) build_vcf_allele() (gpf.variants.core.Allele static method)

C

CACHE_LOCK (gpf.pheno.registry.PhenoRegistry attribute) calc() (gpf.pheno_tool.tool.PhenoTool method) calc_alleles() (gpf.variants.family_variant.FamilyVariant static method) calc_alt_alleles() (gpf.variants.family_variant.FamilyVariant static method) calc_batched_heuristics() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) calc_by_effect() (gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapter method) (gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapterBase method) (pheno_tool_api.adapter.PhenoToolAdapter method) calc_coding_bins() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) calc_enrichment_test() (enrichment_api.enrichment_helper.EnrichmentHelper method) (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground method) (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground method) (gpf.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground method) (gpf.enrichment_tool.samocha_background.SamochaEnrichmentBackground method) calc_expected_observed_pvalue() (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground static method) (gpf.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground static method) calc_family_bins() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) calc_frequency_bins() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) calc_heuristics() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) calc_info_hash() (gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation method) calc_inheritance_trio() (gpf.variants.family_variant.FamilyAllele class method) calc_region_bins() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) calc_regression() (gpf.pheno.utils.lin_regress.LinearRegression method) calc_statistics_hash() (gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation method) calc_variants() (gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapter method) (gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapterBase method) (pheno_tool_api.adapter.PhenoToolAdapter method) (pheno_tool_api.adapter.PhenoToolAdapterBase method) calculate_simple_best_state() (in module gpf.variants.family_variant) can_extend() (gpf.pedigrees.pedigrees.Realization method) categorical (gpf.pheno.common.InferenceConfig attribute) (gpf.pheno.common.MeasureType attribute) categorical_attr() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) categorical_config (gpf.pheno.common.MeasureHistogramConfigs attribute) check_affected_dad_family() (in module gpf.pedigrees.family_tag_builder) check_affected_mom_family() (in module gpf.pedigrees.family_tag_builder) check_affected_prb_family() (in module gpf.pedigrees.family_tag_builder) check_affected_sib_family() (in module gpf.pedigrees.family_tag_builder) check_control_family() (in module gpf.pedigrees.family_tag_builder) check_denovo_trio() (gpf.variants.family_variant.FamilyAllele static method) CHECK_DONE_VERBOSITY (gpf.query_variants.query_runners.QueryResult attribute) check_family_tags_query() (in module gpf.pedigrees.family_tag_builder) check_female_prb_family() (in module gpf.pedigrees.family_tag_builder) check_inheritance_denovo_only() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) check_inheritance_query_value() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) check_male_prb_family() (in module gpf.pedigrees.family_tag_builder) check_mendelian_trio() (gpf.variants.family_variant.FamilyAllele static method) check_missing_dad_family() (in module gpf.pedigrees.family_tag_builder) check_missing_mom_family() (in module gpf.pedigrees.family_tag_builder) check_multiplex_family() (in module gpf.pedigrees.family_tag_builder) check_nuclear_family() (in module gpf.pedigrees.family_tag_builder) check_omission_trio() (gpf.variants.family_variant.FamilyAllele static method) check_quad_family() (in module gpf.pedigrees.family_tag_builder) check_roles_denovo_only() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) check_roles_query_value() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) check_simplex_family() (in module gpf.pedigrees.family_tag_builder) check_tag() (in module gpf.pedigrees.family_tag_builder) check_trio_family() (in module gpf.pedigrees.family_tag_builder) check_unaffected_dad_family() (in module gpf.pedigrees.family_tag_builder) check_unaffected_mom_family() (in module gpf.pedigrees.family_tag_builder) check_unaffected_prb_family() (in module gpf.pedigrees.family_tag_builder) check_unaffected_sib_family() (in module gpf.pedigrees.family_tag_builder) check_variant_types_value() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) checkers (gpf.configuration.gpf_config_parser.GPFConfigValidator attribute) child (gpf.variants.attributes.Role attribute) children_set() (gpf.pedigrees.pedigrees.Individual method) (gpf.pedigrees.pedigrees.IndividualGroup method) (gpf.pedigrees.pedigrees.MatingUnit method) (gpf.pedigrees.pedigrees.SibshipUnit method) children_zygosity (gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute) ChildrenBySex (class in gpf.person_sets) (class in gpf.person_sets.person_sets) ChildrenStats (class in gpf.person_sets) (class in gpf.person_sets.person_sets) chrom (gpf.variants.core.Allele property) (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) (gpf.variants.variant.SummaryVariant property) chromosome (gpf.variants.core.Allele property) (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) (gpf.variants.variant.SummaryVariant property) chromosomes (gpf.variants_loaders.cnv.loader.CNVLoader property) (gpf.variants_loaders.dae.loader.DaeTransmittedLoader property) (gpf.variants_loaders.dae.loader.DenovoLoader property) (gpf.variants_loaders.parquet.loader.ParquetLoader property) (gpf.variants_loaders.raw.loader.VariantsLoader property) (gpf.variants_loaders.raw.loader.VariantsLoaderDecorator property) (gpf.variants_loaders.vcf.loader.SingleVcfLoader property) (gpf.variants_loaders.vcf.loader.VcfLoader property) clear_tags() (gpf.pedigrees.family_tag_builder.FamilyTagsBuilder method) cli() (in module gpf.enrichment_tool.build_coding_length_enrichment_background) (in module gpf.enrichment_tool.build_ur_synonymous_enrichment_background) (in module gpf.enrichment_tool.enrichment_cache_builder) (in module gpf.gpf_instance.adjustments.gpf_instance_adjustments) (in module gpf.parquet.schema2.annotate_schema2_parquet) (in module gpf.tools.reannotate_instance) (in module gpf_web.wgpf) cli_arguments() (gpf.variants_loaders.raw.loader.CLILoader class method) (gpf.variants_loaders.raw.loader.VariantsLoaderDecorator class method) (in module gpf.tools.simple_study_import) cli_cache_repo() (in module gpf.tools.grr_cache_repo) cli_defaults() (gpf.variants_loaders.raw.loader.CLILoader class method) (gpf.variants_loaders.raw.loader.VariantsLoaderDecorator class method) cli_export() (in module gpf.gene_profile.exporter) CLIArgument (class in gpf.variants_loaders.raw.loader) CLIGenotypeStorageContextProvider (class in gpf.genotype_storage.genotype_storage_genomic_context_cli) CLILoader (class in gpf.variants_loaders.raw.loader) close() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) (gpf.gpf_instance.adjustments.adjust_command.AdjustmentsCommand method) (gpf.parquet.schema2.loader.MultiReader method) (gpf.parquet.schema2.loader.Reader method) (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) (gpf.parquet.schema2.variants_parquet_writer.ContinuousParquetFileWriter method) (gpf.parquet.schema2.variants_parquet_writer.VariantsParquetWriter method) (gpf.pedigrees.families_data.FamiliesData method) (gpf.pheno.browser.PhenoBrowser method) (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.prepare_data.PreparePhenoBrowserBase method) (gpf.query_variants.query_runners.QueryResult method) (gpf.query_variants.query_runners.QueryRunner method) (gpf.studies.study.GenotypeData method) (gpf.variants_loaders.cnv.loader.CNVLoader method) (gpf.variants_loaders.dae.loader.DaeTransmittedLoader method) (gpf.variants_loaders.dae.loader.DenovoLoader method) (gpf.variants_loaders.parquet.loader.ParquetLoader method) (gpf.variants_loaders.raw.loader.VariantsLoader method) (gpf.variants_loaders.raw.loader.VariantsLoaderDecorator method) (gpf.variants_loaders.vcf.loader.SingleVcfLoader method) (gpf.variants_loaders.vcf.loader.VcfLoader method) (gpf.variants_loaders.vcf.serializer.VcfSerializer method) cnv (gpf.testing.import_helpers.StudyInputLayout attribute) (gpf.variants.core.Allele.Type attribute) cnv_import() (in module gpf.testing.import_helpers) cnv_liftover_main() (in module gpf.tools.liftover_tools) cnv_study() (in module gpf.testing.import_helpers) CNVLiftoverTool (class in gpf.tools.liftover_tools) CNVLoader (class in gpf.variants_loaders.cnv.loader) coding_bin (gpf.parquet.partition_descriptor.Partition attribute) coding_bins (gpf.query_variants.sql.schema2.sql_query_builder.QueryHeuristics attribute) coding_bins() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) coding_len_background() (in module enrichment_api.tests.conftest) coercers (gpf.configuration.gpf_config_parser.GPFConfigValidator attribute)

collect_child_configs() (gpf.pheno.prepare_data.PreparePhenoBrowserBase method) collect_denovo_events() (gpf.enrichment_tool.genotype_helper.GenotypeHelper static method) collect_directory_configs() (gpf.configuration.gpf_config_parser.GPFConfigParser class method) collect_expectations() (gpf.tools.gpf_validation_runner.MainRunner static method) collect_genotype_data_backgrounds() (enrichment_api.enrichment_helper.EnrichmentHelper method) collect_instruments() (in module gpf.pheno.pheno_import) collect_pedigree_parquet_schema() (in module gpf.parquet.parquet_writer) collect_person_collection_attributes() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) collect_variant_counts() (in module gpf.gene_profile.generate_gene_profile) collections_descriptions (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb property) (gpf.gene_sets.gene_sets_db.GeneSetsDb property) color (gpf.person_sets.person_sets.PersonSetConfig attribute) (gpf.person_sets.PersonSetConfig attribute) column_counts() (in module gpf.pheno.graphs) column_name (gpf.common_reports.denovo_report.EffectCell property) combine() (gpf.pedigrees.families_data.FamiliesData static method) (gpf.person_sets.person_sets.PersonSetCollection static method) (gpf.person_sets.PersonSetCollection static method) (gpf.variants.variant.VariantDesc static method) Command (class in users_api.management.commands.user_set_name) (class in users_api.management.commands.user_setpasswd) (class in users_api.management.commands.users_remove) common_report (gpf.pheno.common.StudyConfig attribute) common_reports_api module common_reports_api.common_reports_helper module common_reports_api.tests module common_reports_api.tests.test_common_reports_api module CommonReport (class in gpf.common_reports.common_report) CommonReportsHelper (class in common_reports_api.common_reports_helper) CommonStudyMixin (class in gpf.studies.study) complex (gpf.variants.core.Allele.Type attribute) compound() (gpf.query_variants.attribute_queries.AttributeQueryTransformerFunction method) (gpf.query_variants.attribute_queries.AttributeQueryTransformerSQL method) (gpf.query_variants.attribute_queries.AttributeQueryTransformerSQLLegacy method) (gpf.query_variants.attribute_queries.CompoundStripTransformer method) (gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method) CompoundStripTransformer (class in gpf.query_variants.attribute_queries) config (studies.study_wrapper.WDAEAbstractStudy property) config_columns (studies.study_wrapper.WDAEAbstractStudy property) config_json() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) ConfigDumper (class in gpf.configuration.study_config_builder) connect() (gpf.duckdb_storage.duckdb_connection_factory.DuckDbConnectionFactory method) (gpf.duckdb_storage.duckdb_genotype_storage.AbstractDuckDbStorage method) (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) connected_components() (gpf.pedigrees.pedigrees.FamilyConnections method) construct_import_annotation_pipeline() (in module gpf.import_tools.import_tools) construct_import_annotation_pipeline_config() (in module gpf.import_tools.import_tools) continuous (gpf.pheno.common.InferenceConfig attribute) (gpf.pheno.common.MeasureType attribute) ContinuousParquetFileWriter (class in gpf.parquet.schema2.parquet_io) (class in gpf.parquet.schema2.variants_parquet_writer) CONTROL (gpf.pedigrees.family.FamilyTag attribute) convert() (in module utils.streaming_response_util) convert_to_float() (in module gpf.pheno.prepare.measure_classifier) convert_to_int() (in module gpf.pheno.prepare.measure_classifier) convert_to_numeric() (in module gpf.pheno.prepare.measure_classifier) convert_to_string() (in module gpf.pheno.prepare.measure_classifier) Convertible (class in gpf.pheno.prepare.measure_classifier) copy() (gpf.pedigrees.families_data.FamiliesData method) (gpf.pedigrees.pedigrees.Realization method) copy_graph() (in module gpf.pedigrees.pedigrees) count_measures() (gpf.pheno.browser.PhenoBrowser method) (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.pheno_data.PhenotypeGroup method) (gpf.pheno.pheno_data.PhenotypeStudy method) count_total (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) count_unique_values (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) count_variant() (gpf.common_reports.denovo_report.EffectCell method) (gpf.common_reports.denovo_report.EffectRow method) (in module gpf.gene_profile.generate_gene_profile) count_with_values (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) count_without_values (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) counter() (gpf.tools.gpf_validation_runner.AbstractRunner method) (gpf.tools.gpf_validation_runner.MainRunner method) CounterBase (class in gpf.enrichment_tool.event_counters) CountError create_and_node() (in module gpf.query_variants.attribute_queries) create_background() (enrichment_api.enrichment_helper.EnrichmentHelper method) create_browser() (gpf.pheno.pheno_data.PhenotypeData static method) create_browser_tables() (gpf.pheno.browser.PhenoBrowser static method) create_counter() (enrichment_api.enrichment_helper.EnrichmentHelper method) create_database_connection() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) (in module gpf.duckdb_storage.duckdb_storage_helpers) create_denovo_gene_set_spec() (in module gpf.gene_sets.denovo_gene_sets_config) create_df() (gpf.pheno_tool.tool.PhenoTool method) create_duckdb_tables() (in module gpf.duckdb_storage.duckdb_storage_helpers) create_empty_collection() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection static method) create_enrichment_description() (enrichment_api.enrichment_builder.EnrichmentBuilder method) create_gp_table() (gpf.gene_profile.db.GeneProfileDBWriter method) create_import_tasks() (in module gpf.pheno.pheno_import) create_memory_connection() (in module gpf.duckdb_storage.duckdb_storage_helpers) create_or_node() (in module gpf.query_variants.attribute_queries) create_parquet_scans_layout_from_layout() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage static method) create_parquet_scans_layout_relative() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) create_reference_allele() (gpf.variants.variant.SummaryAllele static method) create_relative_parquet_scans_layout() (in module gpf.duckdb_storage.duckdb_storage_helpers) create_runner() (gpf.genotype_storage.genotype_storage.GenotypeStorage method) create_s3_attach_db_clause() (in module gpf.duckdb_storage.duckdb_storage_helpers) create_s3_filesystem() (in module gpf.duckdb_storage.duckdb_storage_helpers) create_s3_secret_clause() (in module gpf.duckdb_storage.duckdb_storage_helpers) create_sandwich_instance() (gpf.pedigrees.pedigrees.FamilyConnections method) create_schema2_dataset_layout() (in module gpf.schema2_storage.schema2_layout) create_statistics_build_tasks() (gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation method) create_study_parquet_tables_layout() (in module gpf.duckdb_storage.duckdb_storage_helpers) create_summary_runner() (gpf.genotype_storage.genotype_storage.GenotypeStorage method) create_table() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) (gpf.pheno.common.ImportManifest static method) create_table_layout() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage static method) (in module gpf.duckdb_storage.duckdb_storage_helpers) create_table_partitioned() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) create_tables() (in module gpf.pheno.pheno_import) create_test_study() (in module enrichment_api.tests.conftest) CriteriaFilter (class in gpf.person_filters.person_filters) criterias (gpf.gene_sets.denovo_gene_sets_config.DGSSpec attribute) cshl_format() (in module gpf.variants.variant) cshl_location (gpf.variants.variant.SummaryAllele property) (gpf.variants.variant.SummaryVariant property) cshl_position (gpf.variants.variant.SummaryAllele property) cshl_variant (gpf.variants.variant.SummaryAllele property) (gpf.variants.variant.SummaryVariant property) cshl_variant_full (gpf.variants.variant.SummaryAllele property) (gpf.variants.variant.SummaryVariant property) current_idx (gpf.parquet.schema2.loader.MultiReader property) (gpf.parquet.schema2.loader.Reader property) curve_p0() (gpf.pedigrees.layout.Line method) curve_p1() (gpf.pedigrees.layout.Line method) curve_p2() (gpf.pedigrees.layout.Line method) curve_p3() (gpf.pedigrees.layout.Line method) curve_y_at() (gpf.pedigrees.layout.Line method) curved (gpf.pedigrees.layout.Line property) custom_query_transformer() (in module studies.conftest) custom_response_transformer() (in module studies.conftest) custom_wgpf() (in module datasets_api.tests.conftest) (in module studies.conftest) custom_wgpf_module() (in module datasets_api.tests.conftest) (in module studies.conftest) CustomFormatter (class in gpf_web.default_settings)

D

dad (gpf.variants.attributes.Role attribute) dae (gpf.testing.import_helpers.StudyInputLayout attribute) dae_import() (in module gpf.testing.import_helpers) dae_liftover_main() (in module gpf.tools.liftover_tools) dae_study() (in module gpf.testing.import_helpers) DaeLiftoverTool (class in gpf.tools.liftover_tools) DaeTransmittedFamiliesGenotypes (class in gpf.variants_loaders.dae.loader) DaeTransmittedLoader (class in gpf.variants_loaders.dae.loader) dangling() (gpf.pedigrees.pedigrees.Realization method) dangling_set() (gpf.pedigrees.pedigrees.Realization method) data_dictionary (gpf.pheno.common.PhenoImportConfig attribute) data_reset() (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) DataDictionaryConfig (class in gpf.pheno.common) dataset() (in module studies.tests.test_study_group_person_sets_queries) (in module studies.tests.test_study_wrapper_person_sets) (in module studies.tests.test_study_wrapper_unique_variants_query) DatasetHelpers (class in gpf.tools.dataset_helpers) datasets_api module datasets_api.migrations module datasets_api.migrations.0001_initial module datasets_api.migrations.0002_dataset_groups module datasets_api.migrations.0003_alter_dataset_options module datasets_api.migrations.0004_dataset_broken module datasets_api.migrations.0005_dataset_dataset_name module datasets_api.migrations.0006_datasethierarchy module datasets_api.migrations.0007_datasethierarchy_direct module datasets_api.migrations.0008_datasethierarchy_instance_id module datasets_api.tests module datasets_api.tests.conftest module db (gpf.duckdb_storage.duckdb_storage_config.DuckDbConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (gpf.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute) Db2Layout (class in gpf.query_variants.sql.schema2.sql_query_builder) db_name (gpf.pheno.pheno_import.MeasureReport attribute) default (gpf.person_sets.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.PersonSetCollectionConfig attribute) DEFAULT_COMPRESSION (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter attribute) (gpf.parquet.schema2.variants_parquet_writer.ContinuousParquetFileWriter attribute) default_setters (gpf.configuration.gpf_config_parser.GPFConfigValidator attribute) DefaultBox (class in gpf.configuration.gpf_config_parser) DefaultGenotypeStorage (class in gpf.gpf_instance.adjustments.gpf_instance_adjustments) degree() (gpf.pedigrees.pedigrees.Realization method) del_loader_prefix() (gpf.import_tools.import_tools.ImportProject static method) DeleteAttributesFromVariantFilter (class in gpf.parquet.schema2.processing_pipeline) DeleteAttributesFromVariantsBatchFilter (class in gpf.parquet.schema2.processing_pipeline) delimiter (gpf.pheno.common.DataDictionaryConfig attribute) (gpf.pheno.common.InstrumentConfig attribute) (gpf.pheno.common.InstrumentDictionaryConfig attribute) (gpf.pheno.common.PhenoImportConfig attribute) (gpf.pheno.pheno_import.ImportInstrument attribute) denovo (gpf.testing.import_helpers.StudyInputLayout attribute) (gpf.variants.attributes.Inheritance attribute) (gpf.variants.attributes.TransmissionType attribute) denovo_1() (in module enrichment_api.tests.test_t4c8_enrichment) denovo_gene_sets_db (gpf.gpf_instance.gpf_instance.GPFInstance property) (gpf.gpf_instance.GPFInstance property) denovo_gene_sets_types (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb property) denovo_import() (in module gpf.testing.import_helpers) denovo_liftover_main() (in module gpf.tools.liftover_tools) denovo_study() (in module gpf.testing.import_helpers) DenovoFamiliesGenotypes (class in gpf.variants_loaders.dae.loader) DenovoGeneSetCollection (class in gpf.gene_sets.denovo_gene_set_collection) DenovoGeneSetHelpers (class in gpf.gene_sets.denovo_gene_set_helpers) DenovoGeneSetsConfig (class in gpf.gene_sets.denovo_gene_sets_config) DenovoGeneSetsDb (class in gpf.gene_sets.denovo_gene_sets_db) DenovoLiftoverTool (class in gpf.tools.liftover_tools) DenovoLoader (class in gpf.variants_loaders.dae.loader) DenovoReport (class in gpf.common_reports.denovo_report) DenovoReportTable (class in gpf.common_reports.denovo_report) dependencies (datasets_api.migrations.0001_initial.Migration attribute) (datasets_api.migrations.0002_dataset_groups.Migration attribute) (datasets_api.migrations.0003_alter_dataset_options.Migration attribute) (datasets_api.migrations.0004_dataset_broken.Migration attribute) (datasets_api.migrations.0005_dataset_dataset_name.Migration attribute) (datasets_api.migrations.0006_datasethierarchy.Migration attribute) (datasets_api.migrations.0007_datasethierarchy_direct.Migration attribute) (datasets_api.migrations.0008_datasethierarchy_instance_id.Migration attribute) (query_state_save.migrations.0001_initial.Migration attribute) (query_state_save.migrations.0002_auto_20190205_0736.Migration attribute) (query_state_save.migrations.0003_querystate_origin_querystate_timestamp.Migration attribute) (user_queries.migrations.0001_initial.Migration attribute) (users_api.migrations.0001_initial.Migration attribute) (users_api.migrations.0002_auto_20190424_0751.Migration attribute) (users_api.migrations.0003_authenticationlog.Migration attribute) (users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more.Migration attribute) (users_api.migrations.0005_gpuserstate.Migration attribute)

description (gpf.genomic_scores.scores.ScoreDesc attribute) (gpf.studies.study.CommonStudyMixin property) (studies.study_wrapper.WDAEAbstractStudy property) (studies.study_wrapper.WDAEStudy property) description_column (gpf.pheno.common.DataDictionaryConfig attribute) (gpf.pheno.common.InstrumentDictionaryConfig attribute) deselected_family_tags (gpf.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute) deserialize_family_record() (gpf.parquet.schema2.serializers.JsonVariantsDataSerializer method) (gpf.parquet.schema2.serializers.VariantsDataSerializer method) deserialize_family_variant() (gpf.query_variants.base_query_variants.QueryVariantsBase method) deserialize_summary_record() (gpf.parquet.schema2.serializers.JsonVariantsDataSerializer method) (gpf.parquet.schema2.serializers.VariantsDataSerializer method) deserialize_summary_variant() (gpf.query_variants.base_query_variants.QueryVariantsBase method) destination (gpf.pheno.common.PhenoImportConfig attribute) DestinationConfig (class in gpf.pheno.common) details (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.variant.SummaryAllele property) (gpf.variants.variant.SummaryVariant property) determine_destination() (in module gpf.pheno.pheno_import) determine_histogram_type() (in module gpf.pheno.prepare.measure_classifier) DGSCQuery (class in gpf.gene_sets.denovo_gene_sets_config) DGSSpec (class in gpf.gene_sets.denovo_gene_sets_config) Dialect (class in gpf.query_variants.sql.schema2.base_query_builder) dictionary (gpf.pheno.common.InstrumentDescriptionsConfig attribute) (gpf.pheno.common.MeasureDescriptionsConfig attribute) diff() (gpf.pedigrees.family.Person method) disable_study_config() (gpf.tools.dataset_helpers.DatasetHelpers method) display_name (gpf.pheno.common.RegressionMeasure attribute) (gpf.variants.attributes.Role property) DISPLAY_NAME_TYPE (gpf.variants.core.Allele attribute) do_measure_build() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method) do_study_config() (gpf.duckdb_storage.duckdb_import_storage.AbstractDuckDbImportStorage class method) domain (gpf.person_sets.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.PersonSetCollectionConfig attribute) (gpf.pheno.pheno_data.Measure property) domain_json() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) download_sources() (in module genotype_browser.tests.conftest) draw() (gpf.pedigrees.drawing.OffsetLayoutDrawer method) draw_categorical_violin_distribution() (in module gpf.pheno.graphs) draw_families() (in module gpf.tools.draw_pedigree) draw_families_report() (in module gpf.tools.draw_pedigree) draw_linregres() (in module gpf.pheno.graphs) draw_measure_violinplot() (in module gpf.pheno.graphs) draw_ordinal_violin_distribution() (in module gpf.pheno.graphs) draw_pedigree() (in module gpf.tools.draw_pedigree) drop_gp_table() (gpf.gene_profile.db.GeneProfileDBWriter method) DuckDb2Runner (class in gpf.duckdb_storage.duckdb2_variants) DuckDb2Variants (class in gpf.duckdb_storage.duckdb2_variants) duckdb_connect() (in module gpf.duckdb_storage.duckdb_legacy_genotype_storage) duckdb_parquet_storage_factory() (in module gpf.duckdb_storage.duckdb_genotype_storage) duckdb_s3_parquet_storage_factory() (in module gpf.duckdb_storage.duckdb_genotype_storage) duckdb_s3_storage_factory() (in module gpf.duckdb_storage.duckdb_genotype_storage) duckdb_storage_factory() (in module gpf.duckdb_storage.duckdb_genotype_storage) DuckDbBaseConf (class in gpf.duckdb_storage.duckdb_storage_config) DuckDbConf (class in gpf.duckdb_storage.duckdb_storage_config) DuckDbConnectionFactory (class in gpf.duckdb_storage.duckdb_connection_factory) DuckDbImportStorage (class in gpf.duckdb_storage.duckdb_import_storage) DuckDbLegacyImportStorage (class in gpf.duckdb_storage.duckdb_import_storage) DuckDbLegacyStorage (class in gpf.duckdb_storage.duckdb_legacy_genotype_storage) DuckDbParquetConf (class in gpf.duckdb_storage.duckdb_storage_config) DuckDbParquetImportStorage (class in gpf.duckdb_storage.duckdb_import_storage) DuckDbParquetStorage (class in gpf.duckdb_storage.duckdb_genotype_storage) DuckDbQueryDialect (class in gpf.duckdb_storage.duckdb_variants) DuckDbRunner (class in gpf.duckdb_storage.duckdb_variants) DuckDbS3Conf (class in gpf.duckdb_storage.duckdb_storage_config) DuckDbS3ImportStorage (class in gpf.duckdb_storage.duckdb_import_storage) DuckDbS3ParquetConf (class in gpf.duckdb_storage.duckdb_storage_config) DuckDbS3ParquetImportStorage (class in gpf.duckdb_storage.duckdb_import_storage) DuckDbS3ParquetStorage (class in gpf.duckdb_storage.duckdb_genotype_storage) DuckDbS3Storage (class in gpf.duckdb_storage.duckdb_genotype_storage) DuckDbStorage (class in gpf.duckdb_storage.duckdb_genotype_storage) DuckDbVariants (class in gpf.duckdb_storage.duckdb_variants)

E

effect (gpf.enrichment_tool.genotype_helper.GeneEffect attribute) effect_gene_symbols (gpf.variants.variant.SummaryAllele property) (gpf.variants.variant.SummaryVariant property) effect_genes (gpf.enrichment_tool.genotype_helper.AlleleEvent attribute) (gpf.variants.variant.SummaryAllele property) effect_types (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) (gpf.variants.variant.SummaryAllele property) (gpf.variants.variant.SummaryVariant property) effect_types() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) EffectCell (class in gpf.common_reports.denovo_report) EffectRow (class in gpf.common_reports.denovo_report) effects (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (gpf.gene_sets.denovo_gene_sets_config.EffectsCriteria attribute) (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.variant.SummaryAllele property) (gpf.variants.variant.SummaryVariant property) EffectsCriteria (class in gpf.gene_sets.denovo_gene_sets_config) enabled (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) EnableDisableStudies (class in gpf.gpf_instance.adjustments.gpf_instance_adjustments) end (gpf.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.SingleCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.TripleCriteria attribute) end_position (gpf.variants.core.Allele property) (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) (gpf.variants.variant.SummaryVariant property) endpoint_url (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute) enforce_csrf() (utils.authentication.SessionAuthenticationWithoutCSRF method) enrichment_api module enrichment_api.enrichment_builder module enrichment_api.enrichment_helper module enrichment_api.enrichment_serializer module enrichment_api.tests module enrichment_api.tests.conftest module enrichment_api.tests.test_enrichment_api module enrichment_api.tests.test_enrichment_builder module

enrichment_api.tests.test_enrichment_helper_simple module enrichment_api.tests.test_enrichment_serializer module enrichment_api.tests.test_t4c8_enrichment module enrichment_builder() (in module enrichment_api.tests.conftest) enrichment_cache_path (studies.study_wrapper.WDAEAbstractStudy property) enrichment_config (studies.study_wrapper.WDAEAbstractStudy property) enrichment_helper() (in module enrichment_api.tests.conftest) enrichment_serializer() (in module enrichment_api.tests.conftest) enrichment_test() (enrichment_api.enrichment_builder.BaseEnrichmentBuilder method) (enrichment_api.enrichment_builder.EnrichmentBuilder method) EnrichmentBackgroundResourceImplementation (class in gpf.enrichment_tool.resource_implementations.enrichment_resource_impl) EnrichmentBuilder (class in enrichment_api.enrichment_builder) EnrichmentHelper (class in enrichment_api.enrichment_helper) EnrichmentResult (class in gpf.enrichment_tool.event_counters) EnrichmentSerializer (class in enrichment_api.enrichment_serializer) EnrichmentSingleResult (class in gpf.enrichment_tool.event_counters) ERROR (gpf.tools.gpf_validation_runner.TestStatus attribute) error_case_count (gpf.tools.gpf_validation_runner.AbstractRunner property) errors_case_count (gpf.tools.gpf_validation_runner.MainRunner property) escape_char() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method) (gpf.query_variants.sql.schema2.base_query_builder.Dialect static method) escape_quote_char() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method) (gpf.query_variants.sql.schema2.base_query_builder.Dialect static method) event_counts() (gpf.enrichment_tool.event_counters.CounterBase method) EventCountersResult (class in gpf.enrichment_tool.event_counters) events() (gpf.enrichment_tool.event_counters.CounterBase method) (gpf.enrichment_tool.event_counters.EventsCounter method) (gpf.enrichment_tool.event_counters.GeneEventsCounter method) EventsCounter (class in gpf.enrichment_tool.event_counters) EventsResult (class in gpf.enrichment_tool.event_counters) execute() (gpf.gpf_instance.adjustments.adjust_command.AdjustmentsCommand method) (gpf.gpf_instance.adjustments.adjust_duckdb_storage.AdjustDuckDbStorageCommand method) (gpf.gpf_instance.adjustments.adjust_impala_storage.AdjustImpalaStorageCommand method) (gpf.gpf_instance.adjustments.gpf_instance_adjustments.DefaultGenotypeStorage method) (gpf.gpf_instance.adjustments.gpf_instance_adjustments.EnableDisableStudies method) (gpf.gpf_instance.adjustments.gpf_instance_adjustments.InstanceIdCommand method) expand_gene_set() (in module utils.expand_gene_set) expand_gene_syms() (in module utils.expand_gene_set) extend() (gpf.pedigrees.pedigrees.Realization method) extract_person_set_collection_query() (studies.query_transformer.QueryTransformer method) (studies.study_wrapper.QueryTransformerProtocol method)

F

F (gpf.variants.attributes.Sex attribute) f1_trio() (in module enrichment_api.tests.conftest) f1_trio_variants() (in module enrichment_api.tests.conftest) FAIL (gpf.tools.gpf_validation_runner.TestStatus attribute) failed_case_count (gpf.tools.gpf_validation_runner.AbstractRunner property) (gpf.tools.gpf_validation_runner.MainRunner property) families (gpf.pheno.pheno_data.PhenotypeData property) (gpf.pheno.pheno_data.PhenotypeGroup property) (gpf.pheno.pheno_data.PhenotypeStudy property) (gpf.query_variants.base_query_variants.QueryVariants property) (gpf.studies.study.GenotypeData property) (gpf.studies.study.GenotypeDataGroup property) (gpf.studies.study.GenotypeDataStudy property) (studies.study_wrapper.WDAEAbstractStudy property) families_of_persons() (gpf.pedigrees.families_data.FamiliesData method) FamiliesData (class in gpf.pedigrees.families_data) FamiliesGenotypes (class in gpf.variants_loaders.raw.loader) FamiliesGroupCounters (class in gpf.common_reports.family_counter) FamiliesLoader (class in gpf.pedigrees.loader) FamiliesReport (class in gpf.common_reports.family_report) Family (class in gpf.pedigrees.family) family (gpf.common_reports.family_counter.FamilyCounter property) (gpf.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute) (gpf.schema2_storage.schema2_layout.Schema2DatasetLayout attribute) family_allele_indexes (gpf.variants.family_variant.FamilyVariant property) family_alleles (gpf.variants.family_variant.FamilyVariant property) family_alt_alleles (gpf.variants.family_variant.FamilyVariant property) family_api module family_api.tests module family_api.tests.test_family_api module family_attributes (gpf.variants.family_variant.FamilyAllele property) family_base() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) family_best_state (gpf.variants.family_variant.FamilyVariant property) family_bin (gpf.parquet.partition_descriptor.Partition attribute) (gpf.pedigrees.family.Person property) FAMILY_BIN_HEURISTIC_CUTOFF (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase attribute) family_bins (gpf.query_variants.sql.schema2.sql_query_builder.QueryHeuristics attribute) family_bins() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) FAMILY_COLUMNS (gpf.parquet.schema2.loader.ParquetLoader attribute) family_genotype (gpf.variants.family_variant.FamilyVariant property) family_genotype_iterator() (gpf.variants_loaders.dae.loader.DaeTransmittedFamiliesGenotypes method) (gpf.variants_loaders.dae.loader.DenovoFamiliesGenotypes method) (gpf.variants_loaders.raw.loader.FamiliesGenotypes method) (gpf.variants_loaders.vcf.loader.VcfFamiliesGenotypes method) family_id (gpf.enrichment_tool.genotype_helper.VariantEvent attribute) (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) family_ids() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) family_index (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) family_partition() (gpf.parquet.partition_descriptor.PartitionDescriptor method) family_partition_schema() (gpf.parquet.partition_descriptor.PartitionDescriptor method) family_query() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) family_variant_filter_function() (gpf.inmemory_storage.raw_variants.RawFamilyVariants class method) family_variants (gpf.variants_loaders.raw.loader.FullVariant attribute) family_variants() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) family_variants_iterator() (gpf.inmemory_storage.raw_variants.RawFamilyVariants method) (gpf.variants_loaders.raw.loader.VariantsLoader method) FamilyAllele (class in gpf.variants.family_variant) FamilyAlleleParquetSerializer (class in gpf.parquet.schema2.serializers) FamilyConnections (class in gpf.pedigrees.pedigrees) FamilyCounter (class in gpf.common_reports.family_counter) FamilyFilter (class in gpf.person_filters) (class in gpf.person_filters.person_filters) FamilyQueryBuilder (class in gpf.query_variants.sql.schema2.family_builder) FamilyRoleBuilder (class in gpf.pedigrees.family_role_builder) FamilyTag (class in gpf.pedigrees.family) FamilyTagsBuilder (class in gpf.pedigrees.family_tag_builder) FamilyVariant (class in gpf.variants.family_variant) favicon() (in module gpfjs.views) female (gpf.enrichment_tool.event_counters.EnrichmentResult attribute) (gpf.enrichment_tool.event_counters.EventCountersResult attribute) (gpf.enrichment_tool.event_counters.EventsResult attribute) (gpf.enrichment_tool.event_counters.VariantEventsResult attribute) (gpf.person_sets.ChildrenBySex attribute) (gpf.person_sets.ChildrenStats attribute) (gpf.person_sets.person_sets.ChildrenBySex attribute) (gpf.person_sets.person_sets.ChildrenStats attribute) (gpf.variants.attributes.Sex attribute) FEMALE_PRB (gpf.pedigrees.family.FamilyTag attribute) females_count() (gpf.pheno.graphs.GraphColumn method) fetch() (gpf.parquet.schema2.processing_pipeline.Schema2SummaryVariantsBatchSource method) (gpf.parquet.schema2.processing_pipeline.Schema2SummaryVariantsSource method) (gpf.parquet.schema2.processing_pipeline.VariantsLoaderBatchSource method) (gpf.parquet.schema2.processing_pipeline.VariantsLoaderSource method) (gpf.variants_loaders.raw.loader.VariantsLoader method) fetch_annotation() (gpf.duckdb_storage.duckdb2_variants.DuckDb2Variants method) fetch_family_variants() (gpf.parquet.schema2.loader.ParquetLoader method) (gpf.variants_loaders.raw.loader.VariantsLoader method) fetch_summary_variants() (gpf.parquet.schema2.loader.ParquetLoader method) (gpf.variants_loaders.raw.loader.VariantsLoader method) fetch_variants() (gpf.parquet.schema2.loader.ParquetLoader method) fgt2str() (in module gpf.utils.variant_utils) figure_filepath() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method) filename (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentResourceBackground property) (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property) files (gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation property) (gpf.pheno.common.InstrumentDescriptionsConfig attribute) (gpf.pheno.common.MeasureDescriptionsConfig attribute) (gpf.pheno.pheno_import.ImportInstrument attribute) filetype_parsers (gpf.configuration.gpf_config_parser.GPFConfigParser attribute) fill_family_bins() (in module gpf.parquet.parquet_writer) filter() (gpf.parquet.schema2.processing_pipeline.AnnotationPipelineVariantsBatchFilter method) (gpf.parquet.schema2.processing_pipeline.AnnotationPipelineVariantsFilter method) (gpf.parquet.schema2.processing_pipeline.DeleteAttributesFromVariantFilter method) (gpf.parquet.schema2.processing_pipeline.DeleteAttributesFromVariantsBatchFilter method) (gpf.parquet.schema2.variants_parquet_writer.Schema2SummaryVariantBatchConsumer method) (gpf.parquet.schema2.variants_parquet_writer.Schema2SummaryVariantConsumer method) (gpf.parquet.schema2.variants_parquet_writer.Schema2VariantBatchConsumer method) (gpf.parquet.schema2.variants_parquet_writer.Schema2VariantConsumer method)

filter_allele() (gpf.inmemory_storage.raw_variants.RawFamilyVariants class method) filter_denovo_one_event_per_family() (in module gpf.enrichment_tool.event_counters) filter_denovo_one_gene_per_events() (in module gpf.enrichment_tool.event_counters) filter_denovo_one_gene_per_recurrent_events() (in module gpf.enrichment_tool.event_counters) filter_family_variant() (gpf.inmemory_storage.raw_variants.RawFamilyVariants class method) filter_gene_effects() (gpf.inmemory_storage.raw_variants.RawFamilyVariants static method) filter_overlapping_events() (in module gpf.enrichment_tool.event_counters) filter_real_attr() (gpf.inmemory_storage.raw_variants.RawFamilyVariants static method) filter_regions() (gpf.inmemory_storage.raw_variants.RawFamilyVariants static method) FILTER_RENAMES_MAP (studies.query_transformer.QueryTransformer attribute) filter_summary_allele() (gpf.inmemory_storage.raw_variants.RawFamilyVariants class method) filter_summary_variant() (gpf.inmemory_storage.raw_variants.RawFamilyVariants class method) find_dataset_id_in_dict() (in module utils.datasets) find_dataset_id_in_request() (in module utils.datasets) find_genotype_data_config() (gpf.tools.dataset_helpers.DatasetHelpers method) find_genotype_data_config_file() (gpf.tools.dataset_helpers.DatasetHelpers method) find_instrument_values_tables() (gpf.pheno.db.PhenoDb method) find_storage() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) flexible_cnv_loader() (in module gpf.variants_loaders.cnv.flexible_cnv_loader) flexible_denovo_load() (gpf.variants_loaders.dae.loader.DenovoLoader method) flexible_pedigree_read() (gpf.pedigrees.loader.FamiliesLoader static method) flexible_variant_loader() (in module gpf.variants_loaders.raw.flexible_variant_loader) float_type() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method) (gpf.query_variants.sql.schema2.base_query_builder.Dialect static method) fmt_invert (gpf_web.default_settings.CustomFormatter attribute) fmt_normal (gpf_web.default_settings.CustomFormatter attribute) foobar_gpf() (in module gpf.testing.foobar_import) force_extend() (gpf.pedigrees.pedigrees.Realization method) force_type_inference() (in module gpf.pheno.prepare.measure_classifier) format() (gpf_web.default_settings.CustomFormatter method) FORMATS (gpf_web.default_settings.CustomFormatter attribute) frequencies (gpf.variants.variant.SummaryVariant property) frequency (gpf.variants.variant.SummaryAllele property) frequency() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) frequency_bin (gpf.parquet.partition_descriptor.Partition attribute) frequency_bins (gpf.query_variants.sql.schema2.sql_query_builder.QueryHeuristics attribute) frequency_bins() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) from_ (gpf.person_sets.person_sets.SourceConfig attribute) (gpf.person_sets.SourceConfig attribute) from_cnv() (gpf.variants.variant.VariantDetails static method) from_config() (gpf.pheno.storage.PhenotypeStorage static method) from_dict() (gpf.configuration.study_config_builder.TOMLDict static method) from_events_result() (gpf.enrichment_tool.event_counters.EventCountersResult static method) from_families() (gpf.common_reports.family_counter.FamiliesGroupCounters static method) (gpf.pedigrees.families_data.FamiliesData static method) (gpf.person_sets.person_sets.PersonSetCollection static method) (gpf.person_sets.PersonSetCollection static method) from_families_data() (gpf.common_reports.family_report.FamiliesReport static method) from_family() (gpf.common_reports.family_counter.FamilyCounter static method) (gpf.pedigrees.layout.Layout static method) (gpf.pedigrees.pedigrees.FamilyConnections class method) from_family_layout() (gpf.pedigrees.layout.Layout static method) from_family_persons() (gpf.pedigrees.families_data.FamiliesData static method) from_genotype_study() (gpf.common_reports.denovo_report.DenovoReport static method) from_json() (gpf.genomic_scores.scores.ScoreDesc static method) (gpf.person_sets.person_sets.PersonSet static method) (gpf.person_sets.PersonSet static method) (gpf.pheno.pheno_data.Measure class method) from_label() (gpf.pedigrees.family.FamilyTag static method) from_list() (gpf.configuration.study_config_builder.TOMLList static method) from_name() (gpf.variants.attributes.Inheritance static method) (gpf.variants.attributes.Role static method) (gpf.variants.attributes.Sex static method) (gpf.variants.attributes.Status static method) (gpf.variants.attributes.Zygosity static method) from_pedigree_df() (gpf.pedigrees.families_data.FamiliesData static method) from_person_set() (gpf.common_reports.people_counter.PeopleCounter static method) from_person_set_collection() (gpf.common_reports.people_counter.PeopleCounters static method) from_person_set_collections() (gpf.common_reports.people_counter.PeopleReport static method) from_persons() (gpf.pedigrees.family.Family static method) from_pylist() (gpf.parquet.partition_descriptor.Partition static method) from_record() (gpf.pheno.pheno_data.Measure class method) from_records() (gpf.pedigrees.family.Family static method) from_row() (gpf.pheno.common.ImportManifest static method) from_sets() (gpf.pedigrees.pedigrees.SandwichInstance static method) from_str() (gpf.pheno.common.MeasureType static method) from_study() (gpf.common_reports.family_report.FamiliesReport static method) from_table() (gpf.pheno.common.ImportManifest static method) from_value() (gpf.variants.attributes.Inheritance static method) (gpf.variants.attributes.Role static method) (gpf.variants.attributes.Sex static method) (gpf.variants.attributes.Status static method) (gpf.variants.attributes.Zygosity static method) from_variants() (gpf.common_reports.denovo_report.DenovoReportTable static method) from_vcf() (gpf.variants.variant.VariantDetails static method) FrozenBox (class in gpf.configuration.gpf_config_parser) full_members (gpf.pedigrees.family.Family property) full_variants (gpf.inmemory_storage.raw_variants.RawMemoryVariants property) full_variants_iterator() (gpf.inmemory_storage.raw_variants.RawFamilyVariants method) (gpf.inmemory_storage.raw_variants.RawMemoryVariants method) (gpf.variants_loaders.cnv.loader.CNVLoader method) (gpf.variants_loaders.dae.loader.DenovoLoader method) (gpf.variants_loaders.raw.loader.VariantsGenotypesLoader method) (gpf.variants_loaders.raw.loader.VariantsLoader method) FullVariant (class in gpf.variants_loaders.raw.loader) fv1() (in module studies.tests.test_response_transformer_columns) fv2() (in module studies.tests.test_response_transformer_columns) fvuid (gpf.enrichment_tool.genotype_helper.VariantEvent attribute) (gpf.variants.family_variant.FamilyVariant property)

G

GAP (gpf.pedigrees.drawing.OffsetLayoutDrawer attribute) gender_palette() (in module gpf.pheno.graphs) gender_palette_light() (in module gpf.pheno.graphs) gene (gpf.enrichment_tool.genotype_helper.GeneEffect attribute) gene_models (gpf.gpf_instance.gpf_instance.GPFInstance property) (gpf.gpf_instance.GPFInstance property) gene_profiles_api module gene_profiles_api.tests module gene_profiles_api.tests.test_agp_api module gene_profiles_api.tests.test_agp_api_configless module GENE_REGIONS_HEURISTIC_CUTOFF (gpf.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute) (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase attribute) GENE_REGIONS_HEURISTIC_EXTEND (gpf.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute) (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase attribute) gene_scores module gene_scores.tests module gene_scores.tests.conftest module gene_scores.tests.test_gene_scores module gene_scores.tests.test_gene_scores_db module gene_scores.tests.test_gene_scores_views module gene_scores.tests.test_scores_partitions module gene_scores_db (gpf.gpf_instance.gpf_instance.GPFInstance property) (gpf.gpf_instance.GPFInstance property) gene_scores_db() (in module gene_scores.tests.conftest) gene_set_id (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (gpf.gene_sets.denovo_gene_sets_config.DGSSpec attribute) gene_sets module gene_sets.tests module gene_sets.tests.test_gene_sets_api module gene_sets_db (gpf.gpf_instance.gpf_instance.GPFInstance property) (gpf.gpf_instance.GPFInstance property) gene_sets_ids (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) gene_view module gene_view.tests module gene_view.tests.test_gene_view module GeneEffect (class in gpf.enrichment_tool.genotype_helper) GeneEventsCounter (class in gpf.enrichment_tool.event_counters) GeneProfileDB (class in gpf.gene_profile.db) GeneProfileDBWriter (class in gpf.gene_profile.db) generate_gp() (in module gpf.gene_profile.generate_gene_profile) generate_import_manifests() (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.pheno_data.PhenotypeGroup method) (gpf.pheno.pheno_data.PhenotypeStudy method) generate_import_task_graph() (gpf.duckdb_storage.duckdb_import_storage.AbstractDuckDbImportStorage method) (gpf.import_tools.import_tools.ImportStorage method) (gpf.inmemory_storage.inmemory_import_storage.InmemoryImportStorage method) (gpf.parquet_storage.storage.ParquetImportStorage method) (gpf.schema2_storage.schema2_import_storage.Schema2ImportStorage method) generate_instrument_table_name() (in module gpf.pheno.db) generate_phenotype_data_config() (in module gpf.pheno.pheno_import) generate_reannotate_task_graph() (gpf.schema2_storage.schema2_import_storage.Schema2ImportStorage static method) generated (gpf.pedigrees.family.Person property) generation_ranks() (gpf.pedigrees.pedigrees.IndividualGroup method) genes() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) genes_prob() (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground method) (gpf.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground method) genes_weight() (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground method) (gpf.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground method) GeneScoreEnrichmentBackground (class in gpf.enrichment_tool.gene_weights_background) GeneSetsDb (class in gpf.gene_sets.gene_sets_db) genetic_model (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) GeneticModel (class in gpf.variants.attributes) GeneWeightsEnrichmentBackground (class in gpf.enrichment_tool.gene_weights_background) genomes_api module genomes_api.tests module genomes_api.tests.test_gene_models_api module genomic_scores (gpf.gpf_instance.gpf_instance.GPFInstance property) (gpf.gpf_instance.GPFInstance property) genomic_scores_api module genomic_scores_api.tests module genomic_scores_api.tests.test_genomic_scores_api module GenomicScoresRegistry (class in gpf.genomic_scores.scores) genotype (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) genotype_browser module genotype_browser.tests module genotype_browser.tests.conftest module genotype_browser.tests.test_effect_types_download module genotype_browser.tests.test_pheno_columns module genotype_browser.tests.test_pheno_filters module genotype_data (studies.study_wrapper.WDAEAbstractStudy property) genotype_data_persons() (gpf.pheno_tool.tool.PhenoToolHelper method) genotype_data_variants() (gpf.pheno_tool.tool.PhenoToolHelper method) genotype_storages (gpf.gpf_instance.gpf_instance.GPFInstance property) (gpf.gpf_instance.GPFInstance property) GenotypeBrowserRunner (class in gpf.tools.gpf_validation_runner) GenotypeData (class in gpf.studies.study) GenotypeDataGroup (class in gpf.studies.study) GenotypeDataStudy (class in gpf.studies.study) GenotypeHelper (class in gpf.enrichment_tool.genotype_helper) GenotypeStorage (class in gpf.genotype_storage.genotype_storage) GenotypeStorageRegistry (class in gpf.genotype_storage.genotype_storage_registry) get() (gpf.pedigrees.families_data.FamiliesData method) (gpf.studies.variants_db.VariantsDb method) get_active_vertex_edges() (gpf.pedigrees.pedigrees.Realization method) get_active_vertices() (gpf.pedigrees.pedigrees.Realization method) get_all_gene_score_descs() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_all_gene_scores() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_all_gene_sets() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection class method) (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) (gpf.gene_sets.gene_sets_db.GeneSetsDb method) get_all_genotype_data() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) (gpf.studies.variants_db.VariantsDb method) get_all_genotype_group_ids() (gpf.studies.variants_db.VariantsDb method) get_all_genotype_groups() (gpf.studies.variants_db.VariantsDb method) get_all_genotype_storage_ids() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) get_all_genotype_storages() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) get_all_genotype_studies() (gpf.studies.variants_db.VariantsDb method) get_all_genotype_study_ids() (gpf.studies.variants_db.VariantsDb method) get_all_phenotype_data() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) (gpf.pheno.registry.PhenoRegistry method) get_all_phenotype_storage_ids() (gpf.pheno.storage.PhenotypeStorageRegistry method) get_all_phenotype_storages() (gpf.pheno.storage.PhenotypeStorageRegistry method) get_annotatable() (gpf.variants.core.Allele method) get_annotation_pipeline() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_annotation_pipeline_config() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) (gpf.import_tools.import_tools.ImportProject method) get_argument_parser() (gpf.tools.reannotate_instance.ReannotateInstanceTool method) get_attr() (gpf.pedigrees.family.Person method) get_attribute() (gpf.variants.family_variant.FamilyAllele method) (gpf.variants.variant.SummaryAllele method) (gpf.variants.variant.SummaryVariant method) (gpf.variants_loaders.raw.loader.VariantsLoader method) (gpf.variants_loaders.raw.loader.VariantsLoaderDecorator method) get_base_dir() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) get_bbox() (gpf.pedigrees.layout.Layout method) get_cache_path() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_children() (gpf.person_sets.person_sets.PersonSet method) (gpf.person_sets.PersonSet method) get_children_by_sex() (gpf.person_sets.person_sets.PersonSet method) (gpf.person_sets.PersonSet method) get_children_count() (gpf.person_sets.person_sets.PersonSet method) (gpf.person_sets.PersonSet method) get_children_ids() (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.pheno_data.PhenotypeGroup method) (gpf.pheno.pheno_data.PhenotypeStudy method) (gpf.studies.study.GenotypeData method) (gpf.studies.study.GenotypeDataGroup method) (gpf.studies.study.GenotypeDataStudy method) (studies.study_wrapper.WDAEAbstractStudy method) (studies.study_wrapper.WDAEStudyGroup method) get_children_stats() (gpf.person_sets.person_sets.PersonSet method) (gpf.person_sets.PersonSet method) get_clean_config() (in module studies.study_wrapper) get_collection_types_legend() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) get_column_sources() (studies.study_wrapper.WDAEStudy method) get_columns() (gpf.pedigrees.family.Family method) get_columns_as_sources() (studies.study_wrapper.WDAEStudy static method) get_columns_to_draw() (in module gpf.pheno.graphs) get_common_report() (common_reports_api.common_reports_helper.BaseCommonReportsHelper method) (common_reports_api.common_reports_helper.CommonReportsHelper method) (gpf.pheno.pheno_data.PhenotypeData method) (gpf.studies.study.GenotypeData method) get_context_genotype_storages() (in module gpf.genotype_storage.genotype_storage_genomic_context_cli) get_context_keys() (gpf.gpf_instance_plugin.gpf_instance_context_plugin.GPFInstanceGenomicContext method) get_context_object() (gpf.gpf_instance_plugin.gpf_instance_context_plugin.GPFInstanceGenomicContext method) get_count() (pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method) (pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method) get_data_dir() (gpf.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage method) get_dataset() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_db() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) get_db_filename() (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3Storage method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbStorage method) (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) get_default_background_model() (enrichment_api.enrichment_helper.EnrichmentHelper method) get_default_counting_model() (enrichment_api.enrichment_helper.EnrichmentHelper method) get_default_genotype_storage() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) get_default_phenotype_storage() (gpf.pheno.storage.PhenotypeStorageRegistry method) get_denovo_events() (gpf.enrichment_tool.genotype_helper.GenotypeHelper method) get_denovo_gene_set_spec() (in module utils.gene_sets) get_empty() (gpf.common_reports.denovo_report.EffectRow method) get_enrichment_cache_path() (in module gpf.enrichment_tool.enrichment_utils) get_enrichment_config() (in module gpf.enrichment_tool.enrichment_utils) get_enrichment_models() (enrichment_api.enrichment_helper.BaseEnrichmentHelper method) (enrichment_api.enrichment_helper.EnrichmentHelper method) get_family_counter_list() (common_reports_api.common_reports_helper.BaseCommonReportsHelper method) (common_reports_api.common_reports_helper.CommonReportsHelper method) get_family_counter_tsv() (common_reports_api.common_reports_helper.BaseCommonReportsHelper method) (common_reports_api.common_reports_helper.CommonReportsHelper method) get_family_data_tsv() (common_reports_api.common_reports_helper.BaseCommonReportsHelper method) (common_reports_api.common_reports_helper.CommonReportsHelper method) get_family_pedigree() (in module gpf.common_reports.family_counter) get_family_pq_filepaths() (gpf.parquet.schema2.loader.ParquetLoader method) get_family_read_counts() (gpf.variants_loaders.dae.loader.DaeTransmittedFamiliesGenotypes method) get_family_type() (in module gpf.common_reports.family_counter) get_filtered_family_data_tsv() (common_reports_api.common_reports_helper.BaseCommonReportsHelper method) (common_reports_api.common_reports_helper.CommonReportsHelper method) get_full_common_report() (common_reports_api.common_reports_helper.BaseCommonReportsHelper method) (common_reports_api.common_reports_helper.CommonReportsHelper method) get_gene_score() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_gene_score_desc() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_gene_set() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) (gpf.gene_sets.gene_sets_db.GeneSetsDb method) get_gene_set_collection_ids() (gpf.gene_sets.gene_sets_db.GeneSetsDb method) get_gene_set_from_collections() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection class method) get_gene_set_ids() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) (gpf.gene_sets.gene_sets_db.GeneSetsDb method) get_gene_sets_types_legend() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) get_gene_view_summary_variants() (studies.study_wrapper.WDAEAbstractStudy method) (studies.study_wrapper.WDAEStudy method) get_gene_view_summary_variants_download() (studies.study_wrapper.WDAEAbstractStudy method) (studies.study_wrapper.WDAEStudy method) get_genotype_data() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_genotype_data_config() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_genotype_data_ids() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_genotype_group() (gpf.studies.variants_db.VariantsDb method) get_genotype_group_config() (gpf.studies.variants_db.VariantsDb method) get_genotype_storage() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) (gpf.import_tools.import_tools.ImportProject method) (gpf.tools.dataset_helpers.DatasetHelpers method) get_genotype_storage_factory() (in module gpf.genotype_storage.genotype_storage_registry) get_genotype_storage_types() (in module gpf.genotype_storage.genotype_storage_registry) get_genotype_study() (gpf.studies.variants_db.VariantsDb method) get_genotype_study_config() (gpf.studies.variants_db.VariantsDb method) get_gp() (gpf.gene_profile.db.GeneProfileDB method) get_gp_configuration() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_gp_statistic() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_gpf_instance() (gpf.import_tools.import_tools.ImportProject method) (in module gpf.pheno.pheno_import) get_graph() (gpf.pedigrees.pedigrees.FamilyConnections method) get_image() (gpf.pheno.pheno_data.PhenotypeData method) (pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method) (pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method) get_import_storage() (gpf.import_tools.import_tools.ImportProject method) get_import_storage_factory() (in module gpf.import_tools.import_tools) get_import_storage_types() (in module gpf.import_tools.import_tools) get_import_variants_buckets() (gpf.import_tools.import_tools.ImportProject method) get_individual() (gpf.pedigrees.pedigrees.FamilyConnections method) get_individuals() (gpf.pedigrees.pedigrees.FamilyConnections method) get_individuals_with_rank() (gpf.pedigrees.pedigrees.FamilyConnections method) get_info() (gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation method) get_input_filenames() (gpf.import_tools.import_tools.ImportProject method) get_instrument_measures() (gpf.pheno.pheno_data.PhenotypeData method) get_instruments() (gpf.pheno.pheno_data.PhenotypeData method) (pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method) (pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method) get_interval() (gpf.pedigrees.pedigrees.Realization method) get_interval_locus_ploidy() (in module gpf.utils.variant_utils) get_leaf_children() (gpf.studies.study.GenotypeData method) get_leaves() (gpf.pheno.pheno_data.PhenotypeGroup method) get_locus_ploidy() (in module gpf.utils.variant_utils) get_mating_units() (gpf.pedigrees.pedigrees.FamilyConnections method) get_maximal_set() (gpf.pedigrees.pedigrees.Realization method) get_measure() (gpf.pheno.pheno_data.PhenotypeData method) get_measure_description() (gpf.pheno.pheno_data.PhenotypeData method) (pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method) (pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method) get_measure_ids() (pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method) (pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method) get_measures() (gpf.pheno.pheno_data.PhenotypeData method) (studies.study_wrapper.WDAEAbstractStudy method) get_measures_df() (gpf.pheno.db.PhenoDb method) get_measures_info() (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.pheno_data.PhenotypeGroup method) (gpf.pheno.pheno_data.PhenotypeStudy method) (pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method) (pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method) get_measures_json() (studies.study_wrapper.WDAEAbstractStudy method) (studies.study_wrapper.WDAEStudy method) get_member() (gpf.pedigrees.family.Family method) get_members_with_roles() (gpf.pedigrees.family.Family method) get_members_with_statuses() (gpf.pedigrees.family.Family method) get_memory_limit() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) get_normalize_measure_id() (gpf.pheno_tool.tool.PhenoTool method) get_or_create_query_transformer() (in module studies.query_transformer) get_or_create_response_transformer() (in module studies.response_transformer) get_output_parquet_files_dir() (in module gpf.pheno.pheno_import) get_paginated_response() (utils.pagination.WdaePageNumberPagination method) get_parquet_dataset_dir() (gpf.import_tools.import_tools.ImportProject method) get_partition_descriptor() (gpf.import_tools.import_tools.ImportProject method) get_pedigree() (gpf.import_tools.import_tools.ImportProject method) get_pedigree_column_names() (in module gpf.pedigrees.family) get_pedigree_df() (gpf.pheno.db.PhenoDb method) (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.pheno_data.PhenotypeGroup method) (gpf.pheno.pheno_data.PhenotypeStudy method) get_pedigree_filename() (gpf.import_tools.import_tools.ImportProject method) get_pedigree_loader() (gpf.import_tools.import_tools.ImportProject method) get_pedigree_params() (gpf.import_tools.import_tools.ImportProject method) get_people_measure_values() (gpf.pheno.db.PhenoDb method) (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.pheno_data.PhenotypeGroup method) (gpf.pheno.pheno_data.PhenotypeStudy method) get_people_measure_values_df() (gpf.pheno.db.PhenoDb method) (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.pheno_data.PhenotypeGroup method) (gpf.pheno.pheno_data.PhenotypeStudy method) get_person_color() (gpf.person_sets.person_sets.PersonSetCollection static method) (gpf.person_sets.PersonSetCollection static method) get_person_roles() (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.pheno_data.PhenotypeGroup method) get_person_set() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) get_person_set_collection() (gpf.pheno.pheno_data.PhenotypeData method) (gpf.studies.study.GenotypeData method) (studies.study_wrapper.WDAEAbstractStudy method) get_person_set_collection_legend() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) get_person_set_of_person() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) get_persons() (gpf.pheno.pheno_data.PhenotypeData method) get_persons_df() (gpf.pheno.db.PhenoDb method) (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.pheno_data.PhenotypeGroup method) (gpf.pheno.pheno_data.PhenotypeStudy method) get_pheno_browser_images_dir() (in module gpf.pheno.pheno_data) get_pheno_cache_path() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_pheno_db_dir() (in module gpf.pheno.pheno_data) get_phenotype_data() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) (gpf.pheno.registry.PhenoRegistry method) get_phenotype_data_config() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) (gpf.pheno.registry.PhenoRegistry method) get_phenotype_data_ids() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) (gpf.pheno.registry.PhenoRegistry method) get_phenotype_storage() (gpf.pheno.storage.PhenotypeStorageRegistry method) get_processing_annotation_batch_size() (gpf.import_tools.import_tools.ImportProject method) get_processing_parquet_dataset_dir() (gpf.import_tools.import_tools.ImportProject method) get_query_leaf_studies() (gpf.studies.study.GenotypeData method) get_query_person_set_ids() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) get_regression_measures() (gpf.pheno.prepare_data.PreparePhenoBrowserBase method) get_regressions() (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.pheno_data.PhenotypeGroup method) (gpf.pheno.pheno_data.PhenotypeStudy method) get_result_by_sex() (gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapter method) (pheno_tool_api.adapter.PhenoToolAdapter method) get_row_group_size() (gpf.import_tools.import_tools.ImportProject method) get_schema() (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentResourceBackground static method) (gpf.enrichment_tool.samocha_background.SamochaEnrichmentBackground static method) get_scores() (gpf.genomic_scores.scores.GenomicScoresRegistry method) get_selected_counting_models() (enrichment_api.enrichment_helper.EnrichmentHelper method) get_selected_person_set_collections() (enrichment_api.enrichment_helper.EnrichmentHelper method) get_sibship_units() (gpf.pedigrees.pedigrees.FamilyConnections method) get_source() (gpf.gpf_instance_plugin.gpf_instance_context_plugin.GPFInstanceGenomicContext method) get_statistics_info() (gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation method) get_stats() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) get_storage_types() (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbParquetStorage class method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3ParquetStorage class method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3Storage class method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbStorage class method) (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage class method) (gpf.genotype_storage.genotype_storage.GenotypeStorage class method) (gpf.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage class method) (gpf.parquet_storage.storage.ParquetGenotypeStorage class method) get_studies() (gpf_instance.extension.GPFExtensionBase method) get_studies_ids() (gpf.studies.study.GenotypeData method) (gpf.studies.study.GenotypeDataGroup method) (gpf.studies.study.GenotypeDataStudy method) (gpf_instance.extension.GPFExtensionBase method) (studies.study_wrapper.WDAEAbstractStudy method) (studies.study_wrapper.WDAEStudyGroup method) get_study_config_tables() (in module gpf.duckdb_storage.duckdb_storage_helpers) get_summary_pq_filepaths() (gpf.parquet.schema2.loader.ParquetLoader method) get_sym_2_fn() (in module gpf.enrichment_tool.event_counters) get_tool() (gpf_instance.extension.GPFExtensionBase method) get_transcript_models() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_unique_family_variants() (studies.query_transformer.QueryTransformer method) (studies.study_wrapper.QueryTransformerProtocol method) get_variant_loader() (gpf.import_tools.import_tools.ImportProject method) get_variant_loader_chrom_lens() (gpf.import_tools.import_tools.ImportProject method) get_variant_loader_chromosomes() (gpf.import_tools.import_tools.ImportProject method) get_variant_loader_types() (gpf.import_tools.import_tools.ImportProject method) get_variant_params() (gpf.import_tools.import_tools.ImportProject method) get_variant_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor method) get_wgpf_instance() (in module gpf_instance.gpf_instance) get_work_dir() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) gp_from_table_row() (gpf.gene_profile.db.GeneProfileDB method) gp_from_table_row_single_view() (gpf.gene_profile.db.GeneProfileDB method) gpf module gpf.common_reports module gpf.common_reports.common_report module gpf.common_reports.denovo_report module gpf.common_reports.family_counter module gpf.common_reports.family_report module

gpf.common_reports.people_counter module gpf.configuration module gpf.configuration.gpf_config_parser module gpf.configuration.schemas module gpf.configuration.schemas.dae_conf module gpf.configuration.schemas.gene_profile module gpf.configuration.schemas.gene_weights_db module gpf.configuration.schemas.person_sets module gpf.configuration.schemas.phenotype_data module gpf.configuration.schemas.study_config module gpf.configuration.schemas.wdae_study_config module gpf.configuration.study_config_builder module gpf.configuration.utils module gpf.duckdb_storage module gpf.duckdb_storage.duckdb2_variants module gpf.duckdb_storage.duckdb_connection_factory module gpf.duckdb_storage.duckdb_genotype_storage module gpf.duckdb_storage.duckdb_import_storage module gpf.duckdb_storage.duckdb_legacy_genotype_storage module gpf.duckdb_storage.duckdb_storage_config module gpf.duckdb_storage.duckdb_storage_helpers module gpf.duckdb_storage.duckdb_variants module gpf.enrichment_tool module gpf.enrichment_tool.base_enrichment_background module gpf.enrichment_tool.build_coding_length_enrichment_background module gpf.enrichment_tool.build_ur_synonymous_enrichment_background module gpf.enrichment_tool.enrichment_cache_builder module gpf.enrichment_tool.enrichment_utils module gpf.enrichment_tool.event_counters module gpf.enrichment_tool.gene_weights_background module gpf.enrichment_tool.genotype_helper module gpf.enrichment_tool.resource_implementations module gpf.enrichment_tool.resource_implementations.enrichment_resource_impl module gpf.enrichment_tool.samocha_background module gpf.gene_profile module gpf.gene_profile.convert_gene_profile_to_duckdb module gpf.gene_profile.db module gpf.gene_profile.exporter module gpf.gene_profile.generate_gene_profile module gpf.gene_profile.statistic module gpf.gene_sets module gpf.gene_sets.denovo_gene_set_collection module gpf.gene_sets.denovo_gene_set_helpers module gpf.gene_sets.denovo_gene_sets_config module gpf.gene_sets.denovo_gene_sets_db module gpf.gene_sets.gene_sets_db module gpf.genomic_scores module gpf.genomic_scores.scores module gpf.genotype_storage module gpf.genotype_storage.genotype_storage module gpf.genotype_storage.genotype_storage_genomic_context_cli module gpf.genotype_storage.genotype_storage_registry module gpf.gpf_instance module gpf.gpf_instance.adjustments module gpf.gpf_instance.adjustments.adjust_command module gpf.gpf_instance.adjustments.adjust_duckdb_storage module gpf.gpf_instance.adjustments.adjust_impala_storage module gpf.gpf_instance.adjustments.gpf_instance_adjustments module gpf.gpf_instance.gpf_instance module gpf.gpf_instance_plugin module gpf.gpf_instance_plugin.gpf_instance_context_plugin module gpf.import_tools module gpf.import_tools.cli module gpf.import_tools.import_config module gpf.import_tools.import_tools module gpf.inmemory_storage module gpf.inmemory_storage.annotation_serialization module gpf.inmemory_storage.inmemory_genotype_storage module gpf.inmemory_storage.inmemory_import_storage module gpf.inmemory_storage.raw_variants module gpf.parquet module gpf.parquet.helpers module gpf.parquet.parquet_writer module gpf.parquet.partition_descriptor module gpf.parquet.schema2 module gpf.parquet.schema2.annotate_schema2_parquet module gpf.parquet.schema2.loader module gpf.parquet.schema2.merge_parquet module gpf.parquet.schema2.parquet_io module gpf.parquet.schema2.processing_pipeline module gpf.parquet.schema2.serializers module gpf.parquet.schema2.variants_parquet_writer module gpf.parquet_storage module gpf.parquet_storage.storage module gpf.pedigrees module gpf.pedigrees.drawing module gpf.pedigrees.families_data module gpf.pedigrees.family module gpf.pedigrees.family_role_builder module gpf.pedigrees.family_tag_builder module gpf.pedigrees.layout module gpf.pedigrees.loader module gpf.pedigrees.pedigrees module gpf.pedigrees.testing module gpf.person_filters module gpf.person_filters.person_filters module gpf.person_sets module gpf.person_sets.person_sets module gpf.pheno module gpf.pheno.browser module gpf.pheno.build_pheno_browser module gpf.pheno.common module gpf.pheno.db module gpf.pheno.graphs module gpf.pheno.import_tools module gpf.pheno.pheno_data module gpf.pheno.pheno_import module gpf.pheno.prepare module gpf.pheno.prepare.measure_classifier module gpf.pheno.prepare_data module gpf.pheno.registry module gpf.pheno.storage module gpf.pheno.update_pheno_descriptions module gpf.pheno.utils module gpf.pheno.utils.commons module gpf.pheno.utils.lin_regress module gpf.pheno_tool module gpf.pheno_tool.pheno_tool_adapter module gpf.pheno_tool.tool module gpf.query_variants module gpf.query_variants.attribute_queries module gpf.query_variants.base_query_variants module gpf.query_variants.query_runners module gpf.query_variants.sql module gpf.query_variants.sql.schema2 module gpf.query_variants.sql.schema2.base_query_builder module gpf.query_variants.sql.schema2.base_variants module gpf.query_variants.sql.schema2.family_builder module gpf.query_variants.sql.schema2.sql_query_builder module gpf.query_variants.sql.schema2.summary_builder module gpf.schema2_storage module gpf.schema2_storage.schema2_import_storage module gpf.schema2_storage.schema2_layout module gpf.studies module gpf.studies.study module gpf.studies.variants_db module gpf.testing module gpf.testing.acgt_import module gpf.testing.alla_import module gpf.testing.foobar_import module gpf.testing.import_helpers module gpf.testing.setup_helpers module gpf.testing.t4c8_import module gpf.tools module gpf.tools.dae2vcf module gpf.tools.dataset_helpers module gpf.tools.denovo2vcf module gpf.tools.draw_pedigree module gpf.tools.generate_common_report module gpf.tools.generate_denovo_gene_sets module gpf.tools.gpf_convert_study_config module gpf.tools.gpf_validation_runner module gpf.tools.grr_cache_repo module gpf.tools.liftover_tools module gpf.tools.ped2ped module gpf.tools.reannotate_instance module gpf.tools.simple_study_import module gpf.tools.to_gpf_gene_models_format module gpf.tools.vcf2tsv module gpf.utils module gpf.utils.testing module gpf.utils.variant_utils module gpf.variants module gpf.variants.attributes module gpf.variants.core module gpf.variants.family_variant module gpf.variants.variant module gpf.variants_loaders module gpf.variants_loaders.cnv module gpf.variants_loaders.cnv.flexible_cnv_loader module gpf.variants_loaders.cnv.loader module gpf.variants_loaders.dae module gpf.variants_loaders.dae.loader module gpf.variants_loaders.parquet module gpf.variants_loaders.parquet.loader module gpf.variants_loaders.raw module gpf.variants_loaders.raw.flexible_variant_loader module gpf.variants_loaders.raw.loader module gpf.variants_loaders.vcf module gpf.variants_loaders.vcf.loader module gpf.variants_loaders.vcf.serializer module gpf_fixture() (in module studies.tests.test_study_config_genotype_browser_columns) (in module studies.tests.test_study_group_person_sets_queries) gpf_instance module gpf_instance (gpf.pheno.common.PhenoImportConfig attribute) gpf_instance.apps module gpf_instance.extension module gpf_instance.gpf_instance module gpf_instance.tests module gpf_instance.tests.test_genome_view module gpf_instance.tests.test_version_api module gpf_web module gpf_web.default_settings module gpf_web.eager_settings module gpf_web.gunicorn_settings module gpf_web.mypy_settings module gpf_web.remote_settings module gpf_web.settings module gpf_web.silk_settings module gpf_web.wdaemanage module gpf_web.wgpf module gpf_web.wgpf_settings module GPFConfigParser (class in gpf.configuration.gpf_config_parser) GPFConfigValidator (class in gpf.configuration.gpf_config_parser) GPFExtensionBase (class in gpf_instance.extension) GPFInstance (class in gpf.gpf_instance) (class in gpf.gpf_instance.gpf_instance) GPFInstanceConfig (class in gpf.pheno.common) GPFInstanceContextProvider (class in gpf.gpf_instance_plugin.gpf_instance_context_plugin) GPFInstanceGenomicContext (class in gpf.gpf_instance_plugin.gpf_instance_context_plugin) gpfjs module gpfjs.views module GPFOAuth2Authentication (class in utils.authentication) GPFTool (class in gpf_instance.extension) GPStatistic (class in gpf.gene_profile.statistic) GraphColumn (class in gpf.pheno.graphs) grey (gpf_web.default_settings.CustomFormatter attribute) grouping() (gpf.query_variants.attribute_queries.AttributeQueryTransformerFunction method) (gpf.query_variants.attribute_queries.AttributeQueryTransformerSQL method) (gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method) groups_api module groups_api.migrations module groups_api.tests module grr (gpf.gpf_instance.gpf_instance.GPFInstance property) (gpf.gpf_instance.GPFInstance property) grr() (in module enrichment_api.tests.conftest) gt2str() (in module gpf.utils.variant_utils) gt_flatten() (gpf.variants.family_variant.FamilyAllele method) (gpf.variants.family_variant.FamilyVariant method)

H

half_sibling (gpf.variants.attributes.Role attribute) handle() (users_api.management.commands.user_set_name.Command method) (users_api.management.commands.user_setpasswd.Command method) (users_api.management.commands.users_remove.Command method) handle_measure_inference_tasks() (in module gpf.pheno.pheno_import) has_affected_status_queries() (gpf.inmemory_storage.raw_variants.RawMemoryVariants method) (gpf.parquet_storage.storage.ParquetLoaderVariants method) (gpf.query_variants.base_query_variants.QueryVariants method) (gpf.query_variants.base_query_variants.QueryVariantsBase method) has_attr() (gpf.pedigrees.family.Person method) has_attribute() (gpf.variants.family_variant.FamilyAllele method) (gpf.variants.variant.SummaryAllele method) (gpf.variants.variant.SummaryVariant method) has_cnv (gpf.studies.study.GenotypeData property) has_coding_bins() (gpf.parquet.partition_descriptor.PartitionDescriptor method) has_complex (gpf.studies.study.GenotypeData property) has_denovo (gpf.studies.study.GenotypeData property) (gpf.studies.study.GenotypeDataGroup property) has_denovo_variants() (gpf.import_tools.import_tools.ImportProject method) has_family_bins() (gpf.parquet.partition_descriptor.PartitionDescriptor method) has_family_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor method) has_frequency_bins() (gpf.parquet.partition_descriptor.PartitionDescriptor method) has_gene_score() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) has_gene_set_collection() (gpf.gene_sets.gene_sets_db.GeneSetsDb method) has_gene_sets() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) has_genotype_data (studies.study_wrapper.WDAEAbstractStudy property)

has_genotype_storage() (gpf.import_tools.import_tools.ImportProject method) has_instrument_descriptions (gpf.pheno.browser.PhenoBrowser property) has_measure() (gpf.pheno.pheno_data.PhenotypeData method) has_measure_descriptions (gpf.pheno.browser.PhenoBrowser property) has_members() (gpf.pedigrees.family.Family method) has_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor method) has_pheno_data (studies.study_wrapper.WDAEAbstractStudy property) has_phenotype_data() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) (gpf.pheno.registry.PhenoRegistry method) has_region_bins() (gpf.parquet.partition_descriptor.PartitionDescriptor method) has_summary_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor method) has_tag() (gpf.pedigrees.family.Person method) has_transmitted (gpf.studies.study.GenotypeData property) (gpf.studies.study.GenotypeDataGroup property) has_variants() (gpf.import_tools.import_tools.ImportProject method) (gpf.schema2_storage.schema2_layout.Schema2DatasetLayout method) has_zygosity (gpf.studies.study.GenotypeData property) help (gpf.genomic_scores.scores.ScoreDesc attribute) (users_api.management.commands.user_set_name.Command attribute) (users_api.management.commands.user_setpasswd.Command attribute) (users_api.management.commands.users_remove.Command attribute) heterozygous (gpf.variants.attributes.Zygosity attribute) hist (gpf.genomic_scores.scores.ScoreDesc attribute) histogram_configs (gpf.pheno.common.PhenoImportConfig attribute) histogram_type (gpf.pheno.common.InferenceConfig attribute) (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) homozygous (gpf.variants.attributes.Zygosity attribute)

I

id (gpf.duckdb_storage.duckdb_storage_config.DuckDbBaseConf attribute) (gpf.person_sets.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.person_sets.PersonSetConfig attribute) (gpf.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.PersonSetConfig attribute) (gpf.pheno.common.PhenoImportConfig attribute) id_to_position (gpf.pedigrees.layout.Layout property) import_config (gpf.pheno.common.ImportManifest attribute) import_dataset() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) (gpf.parquet_storage.storage.ParquetGenotypeStorage method) import_pheno_data() (in module gpf.pheno.pheno_import) ImportConfigNormalizer (class in gpf.import_tools.import_tools) ImportInstrument (class in gpf.pheno.pheno_import) ImportManifest (class in gpf.pheno.common) ImportProject (class in gpf.import_tools.import_tools) ImportStorage (class in gpf.import_tools.import_tools) include_reference (gpf.import_tools.import_tools.ImportProject property) increase_indent() (gpf.configuration.study_config_builder.ConfigDumper method) indel (gpf.variants.core.Allele.Type attribute) index (gpf.import_tools.import_tools.Bucket attribute) index() (in module gpfjs.views) Individual (class in gpf.pedigrees.pedigrees) individual_set() (gpf.pedigrees.pedigrees.Individual method) (gpf.pedigrees.pedigrees.IndividualGroup method) (gpf.pedigrees.pedigrees.MatingUnit method) (gpf.pedigrees.pedigrees.SibshipUnit method) IndividualGroup (class in gpf.pedigrees.pedigrees) individuals_by_rank (gpf.pedigrees.layout.Layout property) IndividualWithCoordinates (class in gpf.pedigrees.layout) infer_measures() (in module gpf.pheno.pheno_import) inference_config (gpf.pheno.common.PhenoImportConfig attribute) inference_reference_impl() (in module gpf.pheno.prepare.measure_classifier) inference_report (gpf.pheno.pheno_import.MeasureReport attribute) InferenceConfig (class in gpf.pheno.common) InferenceReport (class in gpf.pheno.prepare.measure_classifier) Inheritance (class in gpf.variants.attributes) inheritance() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) inheritance_in_members (gpf.variants.family_variant.FamilyAllele property) init() (gpf.genotype_storage.genotype_storage_genomic_context_cli.CLIGenotypeStorageContextProvider method) (gpf.gpf_instance_plugin.gpf_instance_context_plugin.GPFInstanceContextProvider method) init_normalize_measures() (gpf.pheno_tool.tool.PhenoTool method) init_vcf_loaders() (gpf.variants_loaders.vcf.loader.VcfLoader method) initial (datasets_api.migrations.0001_initial.Migration attribute) (user_queries.migrations.0001_initial.Migration attribute) (users_api.migrations.0001_initial.Migration attribute) InmemoryGenotypeStorage (class in gpf.inmemory_storage.inmemory_genotype_storage) InmemoryImportStorage (class in gpf.inmemory_storage.inmemory_import_storage) input_dir (gpf.import_tools.import_tools.ImportProject property) (gpf.pheno.common.PhenoImportConfig attribute) insert_gp() (gpf.gene_profile.db.GeneProfileDBWriter method) insert_gps() (gpf.gene_profile.db.GeneProfileDBWriter method) instance_path() (in module studies.tests.test_study_wrapper_person_sets) (in module studies.tests.test_study_wrapper_unique_variants_query) InstanceIdCommand (class in gpf.gpf_instance.adjustments.gpf_instance_adjustments) Instrument (class in gpf.pheno.pheno_data) instrument (gpf.pheno.common.DataDictionaryConfig attribute) (gpf.pheno.common.InstrumentConfig attribute) (gpf.pheno.common.InstrumentDictionaryConfig attribute) instrument_column (gpf.pheno.common.DataDictionaryConfig attribute) (gpf.pheno.common.InstrumentDictionaryConfig attribute) instrument_dictionary (gpf.pheno.common.PhenoImportConfig attribute) instrument_files (gpf.pheno.common.PhenoImportConfig attribute) instrument_name (gpf.pheno.common.RegressionMeasure attribute) (gpf.pheno.pheno_import.MeasureReport attribute) InstrumentConfig (class in gpf.pheno.common)

InstrumentDescriptionsConfig (class in gpf.pheno.common) InstrumentDictionaryConfig (class in gpf.pheno.common) instruments (gpf.pheno.pheno_data.PhenotypeData property) int_type() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method) (gpf.query_variants.sql.schema2.base_query_builder.Dialect static method) intersection() (gpf.pedigrees.pedigrees.Interval method) Interval (class in gpf.pedigrees.pedigrees) IntervalForVertex (class in gpf.pedigrees.pedigrees) inverse_curve_p1() (gpf.pedigrees.layout.Line method) inverse_curve_p2() (gpf.pedigrees.layout.Line method) inverse_curve_y_at() (gpf.pedigrees.layout.Line method) is_active_vertex() (gpf.pedigrees.pedigrees.Realization method) is_all_reference_genotype() (in module gpf.utils.variant_utils) is_all_unknown_genotype() (in module gpf.utils.variant_utils) is_browser_outdated() (gpf.pheno.pheno_data.PhenotypeData method) is_cached() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) is_closed() (gpf.query_variants.query_runners.QueryRunner method) is_cnv() (gpf.variants.core.Allele.Type class method) is_connected() (gpf.pedigrees.pedigrees.FamilyConnections method) is_convertible_to_numeric() (in module gpf.pheno.prepare.measure_classifier) is_done() (gpf.query_variants.query_runners.QueryResult method) (gpf.query_variants.query_runners.QueryRunner method) is_email_valid() (in module utils.email_regex) is_empty() (gpf.common_reports.denovo_report.DenovoReport method) (gpf.common_reports.denovo_report.DenovoReportTable method) (gpf.common_reports.denovo_report.EffectCell method) (gpf.common_reports.people_counter.PeopleCounter method) (gpf.parquet.partition_descriptor.Partition method) (gpf.query_variants.sql.schema2.sql_query_builder.QueryHeuristics method) is_empty_field() (gpf.common_reports.people_counter.PeopleCounter method) is_genotype (studies.study_wrapper.WDAEAbstractStudy property) is_group (gpf.pheno.pheno_data.PhenotypeData property) (gpf.pheno.pheno_data.PhenotypeGroup property) (gpf.studies.study.GenotypeData property) (gpf.studies.study.GenotypeDataGroup property) (gpf.studies.study.GenotypeDataStudy property) (studies.study_wrapper.WDAEAbstractStudy property) is_in_interval_order() (gpf.pedigrees.pedigrees.Realization method) is_individual() (gpf.pedigrees.pedigrees.Individual method) (gpf.pedigrees.pedigrees.IndividualGroup method) is_loaded() (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground method) (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground method) (gpf.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground method) (gpf.enrichment_tool.samocha_background.SamochaEnrichmentBackground method) is_maximal() (gpf.pedigrees.pedigrees.Realization method) is_nan() (in module gpf.pheno.prepare.measure_classifier) is_numeric() (gpf.pheno.common.MeasureType static method) is_older_than() (gpf.pheno.common.ImportManifest method) is_password_valid() (in module utils.password_requirements) is_pedigree_only() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) is_phenotype (studies.study_wrapper.WDAEAbstractStudy property) is_read_only() (gpf.duckdb_storage.duckdb_genotype_storage.AbstractDuckDbStorage method) (gpf.genotype_storage.genotype_storage.GenotypeStorage method) is_reference() (gpf.variants.family_variant.FamilyVariant method) is_reference_allele (gpf.variants.variant.SummaryAllele property) is_reference_genotype() (in module gpf.utils.variant_utils) is_row_empty() (gpf.common_reports.denovo_report.EffectRow method) is_started() (gpf.query_variants.query_runners.QueryRunner method) is_text() (gpf.pheno.common.MeasureType static method) is_tr() (gpf.variants.core.Allele.Type class method) is_unknown() (gpf.variants.family_variant.FamilyVariant method) is_unknown_genotype() (in module gpf.utils.variant_utils) is_valid_family() (gpf.pedigrees.pedigrees.FamilyConnections static method) items() (gpf.pedigrees.families_data.FamiliesData method) iterator_to_json() (in module utils.streaming_response_util)

J

jitter (gpf.pheno.common.RegressionMeasure attribute) join_base_url_and_parquet_scan() (in module gpf.duckdb_storage.duckdb_storage_helpers)

join_pheno_df_with_variants() (gpf.pheno_tool.tool.PhenoTool static method) JsonVariantsDataSerializer (class in gpf.parquet.schema2.serializers)

K

keys() (gpf.pedigrees.families_data.FamiliesData method)

L

label (gpf.pedigrees.family.FamilyTag property) (gpf.pheno.graphs.GraphColumn property) large_deletion (gpf.variants.core.Allele.Type attribute) LARGE_DPI (gpf.pheno.prepare_data.PreparePhenoBrowserBase attribute) large_duplication (gpf.variants.core.Allele.Type attribute) large_values_desc (gpf.genomic_scores.scores.ScoreDesc attribute) Layout (class in gpf.pedigrees.layout) layout (gpf.pedigrees.family.Person property) Layout.BBox (class in gpf.pedigrees.layout) layout_parser() (in module gpf.pedigrees.layout) legend_json() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) liftover_variants() (gpf.tools.liftover_tools.CNVLiftoverTool method) (gpf.tools.liftover_tools.DaeLiftoverTool method) (gpf.tools.liftover_tools.DenovoLiftoverTool method) (gpf.tools.liftover_tools.LiftoverTool method) (gpf.tools.liftover_tools.VCFLiftoverTool method) LiftoverTool (class in gpf.tools.liftover_tools) Line (class in gpf.pedigrees.layout) LinearRegression (class in gpf.pheno.utils.lin_regress) list_gp_gene_symbols() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) list_symbols() (gpf.gene_profile.db.GeneProfileDB method) literal() (gpf.query_variants.attribute_queries.AttributeQueryTransformerFunction method) (gpf.query_variants.attribute_queries.AttributeQueryTransformerSQL method) (gpf.query_variants.attribute_queries.AttributeQueryTransformerSQLLegacy method) (gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method) load() (gpf.common_reports.common_report.CommonReport static method) (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground method) (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground method) (gpf.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground method) (gpf.enrichment_tool.samocha_background.SamochaEnrichmentBackground method) (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) (gpf.pedigrees.loader.FamiliesLoader method)

load_collection() (gpf.gene_sets.denovo_gene_set_helpers.DenovoGeneSetHelpers class method) load_collection_from_dict() (gpf.gene_sets.denovo_gene_set_helpers.DenovoGeneSetHelpers class method) load_config() (gpf.configuration.gpf_config_parser.GPFConfigParser class method) load_config_dict() (gpf.configuration.gpf_config_parser.GPFConfigParser class method) load_config_raw() (gpf.configuration.gpf_config_parser.GPFConfigParser class method) load_directory_configs() (gpf.configuration.gpf_config_parser.GPFConfigParser class method) load_from_dir() (gpf.parquet.schema2.loader.ParquetLoader static method) load_histogram_configs() (in module gpf.pheno.pheno_import) load_inference_configs() (in module gpf.pheno.pheno_import) load_instrument_description_file() (in module gpf.pheno.pheno_import) load_instrument_descriptions() (in module gpf.pheno.pheno_import) load_measure_description_file() (in module gpf.pheno.pheno_import) load_measure_descriptions() (in module gpf.pheno.pheno_import) load_meta() (gpf.schema2_storage.schema2_import_storage.Schema2ImportStorage static method) load_object() (in module query_state_save.tests.conftest) load_pedigree_file() (gpf.pedigrees.loader.FamiliesLoader static method) load_schema2_dataset_layout() (in module gpf.schema2_storage.schema2_layout) load_simple_families_file() (gpf.pedigrees.loader.FamiliesLoader static method) load_study_config() (in module gpf.tools.gpf_convert_study_config) loaded_variants (gpf.genotype_storage.genotype_storage.GenotypeStorage property) location (gpf.variants.variant.SummaryVariant property) location_variant_to_vcf_transformer() (in module gpf.variants_loaders.raw.flexible_variant_loader) log_filter() (in module utils.logger)

M

M (gpf.variants.attributes.Sex attribute) main() (gpf.tools.gpf_validation_runner.MainRunner method) (in module gpf.gene_profile.convert_gene_profile_to_duckdb) (in module gpf.gene_profile.generate_gene_profile) (in module gpf.import_tools.cli) (in module gpf.pheno.build_pheno_browser) (in module gpf.pheno.import_tools) (in module gpf.pheno.pheno_import) (in module gpf.pheno.update_pheno_descriptions) (in module gpf.tools.dae2vcf) (in module gpf.tools.denovo2vcf) (in module gpf.tools.draw_pedigree) (in module gpf.tools.generate_common_report) (in module gpf.tools.generate_denovo_gene_sets) (in module gpf.tools.gpf_convert_study_config) (in module gpf.tools.gpf_validation_runner) (in module gpf.tools.ped2ped) (in module gpf.tools.simple_study_import) (in module gpf.tools.to_gpf_gene_models_format) (in module gpf.tools.vcf2tsv) (in module gpf_web.wdaemanage) MainRunner (class in gpf.tools.gpf_validation_runner) make_all_region_bins() (gpf.parquet.partition_descriptor.PartitionDescriptor method) make_coding_bin() (gpf.parquet.partition_descriptor.PartitionDescriptor method) make_config() (studies.study_wrapper.WDAEAbstractStudy static method) make_family_bin() (gpf.parquet.partition_descriptor.PartitionDescriptor method) make_frequency_bin() (gpf.parquet.partition_descriptor.PartitionDescriptor method) make_pedigree_filter() (in module gpf.person_filters) (in module gpf.person_filters.person_filters) make_pheno_filter() (in module gpf.person_filters) (in module gpf.person_filters.person_filters) make_pheno_filter_beta() (in module gpf.person_filters) (in module gpf.person_filters.person_filters) make_query_transformer() (in module studies.query_transformer) make_region_bin() (gpf.parquet.partition_descriptor.PartitionDescriptor method) make_region_bins_regions() (gpf.parquet.partition_descriptor.PartitionDescriptor method) make_response_transformer() (in module studies.response_transformer) make_tool() (common_reports_api.common_reports_helper.CommonReportsHelper static method) (enrichment_api.enrichment_builder.EnrichmentBuilder static method) (enrichment_api.enrichment_helper.EnrichmentHelper static method) (gpf_instance.extension.GPFTool static method) (pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper static method) (pheno_tool_api.adapter.PhenoToolAdapter static method) make_validation_runner() (gpf.tools.gpf_validation_runner.MainRunner method) male (gpf.enrichment_tool.event_counters.EnrichmentResult attribute) (gpf.enrichment_tool.event_counters.EventCountersResult attribute) (gpf.enrichment_tool.event_counters.EventsResult attribute) (gpf.enrichment_tool.event_counters.VariantEventsResult attribute) (gpf.person_sets.ChildrenBySex attribute) (gpf.person_sets.ChildrenStats attribute) (gpf.person_sets.person_sets.ChildrenBySex attribute) (gpf.person_sets.person_sets.ChildrenStats attribute) (gpf.variants.attributes.Sex attribute) male_female_legend() (in module gpf.pheno.graphs) MALE_PRB (gpf.pedigrees.family.FamilyTag attribute) males_count() (gpf.pheno.graphs.GraphColumn method) mat2str() (in module gpf.utils.variant_utils) matched_alleles (gpf.variants.variant.SummaryVariant property) matched_alleles_indexes (gpf.variants.variant.SummaryVariant property) matched_gene_effects (gpf.variants.variant.SummaryVariant property) Matcher (class in gpf.query_variants.attribute_queries) maternal_aunt (gpf.variants.attributes.Role attribute) maternal_cousin (gpf.variants.attributes.Role attribute) maternal_grandfather (gpf.variants.attributes.Role attribute) maternal_grandmother (gpf.variants.attributes.Role attribute) maternal_half_sibling (gpf.variants.attributes.Role attribute) maternal_uncle (gpf.variants.attributes.Role attribute) Mating (class in gpf.pedigrees.family_role_builder) MatingUnit (class in gpf.pedigrees.pedigrees) MAX_CHILD_NUMBER (gpf.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute) max_rank (gpf.pheno.common.RankRange attribute) max_rank() (gpf.pedigrees.pedigrees.FamilyConnections method) max_value (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) max_x (gpf.pedigrees.layout.Layout.BBox attribute) max_y (gpf.pedigrees.layout.Layout.BBox attribute) Measure (class in gpf.pheno.pheno_data) measure_column (gpf.pheno.common.DataDictionaryConfig attribute) measure_name (gpf.pheno.pheno_import.MeasureReport attribute) measure_names (gpf.pheno.common.RegressionMeasure attribute) measure_type (gpf.pheno.pheno_import.MeasureReport attribute) MeasureDescriptionsConfig (class in gpf.pheno.common) MeasureHistogramConfigs (class in gpf.pheno.common) MeasureReport (class in gpf.pheno.pheno_import) measures (gpf.pheno.pheno_data.PhenotypeData property) measures_api module measures_api.tests module measures_api.tests.test_measures_api module measures_count_status() (pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method) (pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method) MeasureType (class in gpf.pheno.common) media_type (sentry.views.PlainTextParser attribute) member_fpids (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) member_has_both_parents() (gpf.pedigrees.family.Family method) member_has_dad() (gpf.pedigrees.family.Family method) member_has_mom() (gpf.pedigrees.family.Family method) member_has_parent() (gpf.pedigrees.family.Family method) member_ids (gpf.pedigrees.family.Family property) (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) member_index (gpf.pedigrees.family.Person property) member_is_child() (gpf.pedigrees.family.Family method) member_is_parent() (gpf.pedigrees.family.Family method) members (gpf.pedigrees.pedigrees.FamilyConnections property) members_in_order (gpf.pedigrees.family.Family property) members_in_order_get_family_structure() (in module studies.response_transformer) members_index() (gpf.pedigrees.family.Family method) memory_limit (gpf.duckdb_storage.duckdb_storage_config.DuckDbBaseConf attribute) mendelian (gpf.variants.attributes.Inheritance attribute) merge_config() (gpf.configuration.gpf_config_parser.GPFConfigParser static method) merge_configs() (gpf.person_sets.person_sets.PersonSetCollection static method) (gpf.person_sets.PersonSetCollection static method) merge_families() (in module gpf.pedigrees.families_data) merge_histogram_configs() (in module gpf.pheno.pheno_import) merge_inference_configs() (in module gpf.pheno.pheno_import) merge_parquet_directory() (in module gpf.parquet.schema2.merge_parquet) merge_parquets() (in module gpf.parquet.helpers) (in module gpf.parquet.schema2.merge_parquet) merge_partitions() (in module gpf.parquet.schema2.annotate_schema2_parquet) merge_variants_parquets() (in module gpf.parquet.parquet_writer) (in module gpf.parquet.schema2.merge_parquet) meta (gpf.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute) (gpf.schema2_storage.schema2_layout.Schema2DatasetLayout attribute) Migration (class in datasets_api.migrations.0001_initial) (class in datasets_api.migrations.0002_dataset_groups) (class in datasets_api.migrations.0003_alter_dataset_options) (class in datasets_api.migrations.0004_dataset_broken) (class in datasets_api.migrations.0005_dataset_dataset_name) (class in datasets_api.migrations.0006_datasethierarchy) (class in datasets_api.migrations.0007_datasethierarchy_direct) (class in datasets_api.migrations.0008_datasethierarchy_instance_id) (class in query_state_save.migrations.0001_initial) (class in query_state_save.migrations.0002_auto_20190205_0736) (class in query_state_save.migrations.0003_querystate_origin_querystate_timestamp) (class in user_queries.migrations.0001_initial) (class in users_api.migrations.0001_initial) (class in users_api.migrations.0002_auto_20190424_0751) (class in users_api.migrations.0003_authenticationlog) (class in users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more) (class in users_api.migrations.0005_gpuserstate) min_individuals (gpf.pheno.common.InferenceConfig attribute) (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) min_rank (gpf.pheno.common.RankRange attribute) min_value (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) min_x (gpf.pedigrees.layout.Layout.BBox attribute) min_y (gpf.pedigrees.layout.Layout.BBox attribute) missing (gpf.pedigrees.family.Person property) (gpf.variants.attributes.Inheritance attribute) MISSING_DAD (gpf.pedigrees.family.FamilyTag attribute) MISSING_MOM (gpf.pedigrees.family.FamilyTag attribute) mock_instance() (in module gpf_instance.tests.test_version_api) model_computed_fields (gpf.duckdb_storage.duckdb_storage_config.DuckDbBaseConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbParquetConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute) (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (gpf.gene_sets.denovo_gene_sets_config.DGSSpec attribute) (gpf.gene_sets.denovo_gene_sets_config.EffectsCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.SexesCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.SingleCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.TripleCriteria attribute) (gpf.person_sets.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.person_sets.PersonSetConfig attribute) (gpf.person_sets.person_sets.SourceConfig attribute) (gpf.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.PersonSetConfig attribute) (gpf.person_sets.SourceConfig attribute) (gpf.pheno.common.DataDictionaryConfig attribute) (gpf.pheno.common.DestinationConfig attribute) (gpf.pheno.common.GPFInstanceConfig attribute) (gpf.pheno.common.ImportManifest attribute) (gpf.pheno.common.InferenceConfig attribute) (gpf.pheno.common.InstrumentConfig attribute) (gpf.pheno.common.InstrumentDescriptionsConfig attribute) (gpf.pheno.common.InstrumentDictionaryConfig attribute) (gpf.pheno.common.MeasureDescriptionsConfig attribute) (gpf.pheno.common.MeasureHistogramConfigs attribute) (gpf.pheno.common.PhenoImportConfig attribute) (gpf.pheno.common.RankRange attribute) (gpf.pheno.common.RegressionMeasure attribute) (gpf.pheno.common.StudyConfig attribute) (gpf.pheno.pheno_import.MeasureReport attribute) (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) (gpf.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute) (gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute) model_config (gpf.duckdb_storage.duckdb_storage_config.DuckDbBaseConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbParquetConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute) (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (gpf.gene_sets.denovo_gene_sets_config.DGSSpec attribute) (gpf.gene_sets.denovo_gene_sets_config.EffectsCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.SexesCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.SingleCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.TripleCriteria attribute) (gpf.person_sets.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.person_sets.PersonSetConfig attribute) (gpf.person_sets.person_sets.SourceConfig attribute) (gpf.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.PersonSetConfig attribute) (gpf.person_sets.SourceConfig attribute) (gpf.pheno.common.DataDictionaryConfig attribute) (gpf.pheno.common.DestinationConfig attribute) (gpf.pheno.common.GPFInstanceConfig attribute) (gpf.pheno.common.ImportManifest attribute) (gpf.pheno.common.InferenceConfig attribute) (gpf.pheno.common.InstrumentConfig attribute) (gpf.pheno.common.InstrumentDescriptionsConfig attribute) (gpf.pheno.common.InstrumentDictionaryConfig attribute) (gpf.pheno.common.MeasureDescriptionsConfig attribute) (gpf.pheno.common.MeasureHistogramConfigs attribute) (gpf.pheno.common.PhenoImportConfig attribute) (gpf.pheno.common.RankRange attribute) (gpf.pheno.common.RegressionMeasure attribute) (gpf.pheno.common.StudyConfig attribute) (gpf.pheno.pheno_import.MeasureReport attribute) (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) (gpf.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute) (gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute) model_fields (gpf.duckdb_storage.duckdb_storage_config.DuckDbBaseConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbParquetConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute) (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (gpf.gene_sets.denovo_gene_sets_config.DGSSpec attribute) (gpf.gene_sets.denovo_gene_sets_config.EffectsCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.SexesCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.SingleCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.TripleCriteria attribute) (gpf.person_sets.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.person_sets.PersonSetConfig attribute) (gpf.person_sets.person_sets.SourceConfig attribute) (gpf.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.PersonSetConfig attribute) (gpf.person_sets.SourceConfig attribute) (gpf.pheno.common.DataDictionaryConfig attribute) (gpf.pheno.common.DestinationConfig attribute) (gpf.pheno.common.GPFInstanceConfig attribute) (gpf.pheno.common.ImportManifest attribute) (gpf.pheno.common.InferenceConfig attribute) (gpf.pheno.common.InstrumentConfig attribute) (gpf.pheno.common.InstrumentDescriptionsConfig attribute) (gpf.pheno.common.InstrumentDictionaryConfig attribute) (gpf.pheno.common.MeasureDescriptionsConfig attribute) (gpf.pheno.common.MeasureHistogramConfigs attribute) (gpf.pheno.common.PhenoImportConfig attribute) (gpf.pheno.common.RankRange attribute) (gpf.pheno.common.RegressionMeasure attribute) (gpf.pheno.common.StudyConfig attribute) (gpf.pheno.pheno_import.MeasureReport attribute) (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) (gpf.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute) (gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute) modify_tuple() (gpf.configuration.gpf_config_parser.GPFConfigParser class method) module common_reports_api common_reports_api.common_reports_helper common_reports_api.tests common_reports_api.tests.test_common_reports_api datasets_api datasets_api.migrations datasets_api.migrations.0001_initial datasets_api.migrations.0002_dataset_groups datasets_api.migrations.0003_alter_dataset_options datasets_api.migrations.0004_dataset_broken datasets_api.migrations.0005_dataset_dataset_name datasets_api.migrations.0006_datasethierarchy datasets_api.migrations.0007_datasethierarchy_direct datasets_api.migrations.0008_datasethierarchy_instance_id datasets_api.tests datasets_api.tests.conftest enrichment_api enrichment_api.enrichment_builder enrichment_api.enrichment_helper enrichment_api.enrichment_serializer enrichment_api.tests enrichment_api.tests.conftest enrichment_api.tests.test_enrichment_api enrichment_api.tests.test_enrichment_builder enrichment_api.tests.test_enrichment_helper_simple enrichment_api.tests.test_enrichment_serializer enrichment_api.tests.test_t4c8_enrichment family_api family_api.tests family_api.tests.test_family_api gene_profiles_api gene_profiles_api.tests gene_profiles_api.tests.test_agp_api gene_profiles_api.tests.test_agp_api_configless gene_scores gene_scores.tests gene_scores.tests.conftest gene_scores.tests.test_gene_scores gene_scores.tests.test_gene_scores_db gene_scores.tests.test_gene_scores_views gene_scores.tests.test_scores_partitions gene_sets gene_sets.tests gene_sets.tests.test_gene_sets_api gene_view gene_view.tests gene_view.tests.test_gene_view genomes_api genomes_api.tests genomes_api.tests.test_gene_models_api genomic_scores_api genomic_scores_api.tests genomic_scores_api.tests.test_genomic_scores_api genotype_browser genotype_browser.tests genotype_browser.tests.conftest genotype_browser.tests.test_effect_types_download genotype_browser.tests.test_pheno_columns genotype_browser.tests.test_pheno_filters gpf gpf.common_reports gpf.common_reports.common_report gpf.common_reports.denovo_report gpf.common_reports.family_counter gpf.common_reports.family_report gpf.common_reports.people_counter gpf.configuration gpf.configuration.gpf_config_parser gpf.configuration.schemas gpf.configuration.schemas.dae_conf gpf.configuration.schemas.gene_profile gpf.configuration.schemas.gene_weights_db gpf.configuration.schemas.person_sets gpf.configuration.schemas.phenotype_data gpf.configuration.schemas.study_config gpf.configuration.schemas.wdae_study_config gpf.configuration.study_config_builder gpf.configuration.utils gpf.duckdb_storage gpf.duckdb_storage.duckdb2_variants gpf.duckdb_storage.duckdb_connection_factory gpf.duckdb_storage.duckdb_genotype_storage gpf.duckdb_storage.duckdb_import_storage gpf.duckdb_storage.duckdb_legacy_genotype_storage gpf.duckdb_storage.duckdb_storage_config gpf.duckdb_storage.duckdb_storage_helpers gpf.duckdb_storage.duckdb_variants gpf.enrichment_tool gpf.enrichment_tool.base_enrichment_background gpf.enrichment_tool.build_coding_length_enrichment_background gpf.enrichment_tool.build_ur_synonymous_enrichment_background gpf.enrichment_tool.enrichment_cache_builder gpf.enrichment_tool.enrichment_utils gpf.enrichment_tool.event_counters gpf.enrichment_tool.gene_weights_background gpf.enrichment_tool.genotype_helper gpf.enrichment_tool.resource_implementations gpf.enrichment_tool.resource_implementations.enrichment_resource_impl gpf.enrichment_tool.samocha_background gpf.gene_profile gpf.gene_profile.convert_gene_profile_to_duckdb gpf.gene_profile.db gpf.gene_profile.exporter gpf.gene_profile.generate_gene_profile gpf.gene_profile.statistic gpf.gene_sets gpf.gene_sets.denovo_gene_set_collection gpf.gene_sets.denovo_gene_set_helpers gpf.gene_sets.denovo_gene_sets_config gpf.gene_sets.denovo_gene_sets_db gpf.gene_sets.gene_sets_db gpf.genomic_scores gpf.genomic_scores.scores gpf.genotype_storage gpf.genotype_storage.genotype_storage gpf.genotype_storage.genotype_storage_genomic_context_cli gpf.genotype_storage.genotype_storage_registry gpf.gpf_instance gpf.gpf_instance.adjustments gpf.gpf_instance.adjustments.adjust_command gpf.gpf_instance.adjustments.adjust_duckdb_storage gpf.gpf_instance.adjustments.adjust_impala_storage gpf.gpf_instance.adjustments.gpf_instance_adjustments gpf.gpf_instance.gpf_instance gpf.gpf_instance_plugin gpf.gpf_instance_plugin.gpf_instance_context_plugin gpf.import_tools gpf.import_tools.cli gpf.import_tools.import_config gpf.import_tools.import_tools gpf.inmemory_storage gpf.inmemory_storage.annotation_serialization gpf.inmemory_storage.inmemory_genotype_storage gpf.inmemory_storage.inmemory_import_storage gpf.inmemory_storage.raw_variants gpf.parquet gpf.parquet.helpers gpf.parquet.parquet_writer gpf.parquet.partition_descriptor gpf.parquet.schema2 gpf.parquet.schema2.annotate_schema2_parquet gpf.parquet.schema2.loader gpf.parquet.schema2.merge_parquet gpf.parquet.schema2.parquet_io gpf.parquet.schema2.processing_pipeline gpf.parquet.schema2.serializers gpf.parquet.schema2.variants_parquet_writer gpf.parquet_storage gpf.parquet_storage.storage gpf.pedigrees gpf.pedigrees.drawing gpf.pedigrees.families_data gpf.pedigrees.family gpf.pedigrees.family_role_builder gpf.pedigrees.family_tag_builder gpf.pedigrees.layout gpf.pedigrees.loader gpf.pedigrees.pedigrees gpf.pedigrees.testing gpf.person_filters gpf.person_filters.person_filters gpf.person_sets gpf.person_sets.person_sets gpf.pheno gpf.pheno.browser gpf.pheno.build_pheno_browser gpf.pheno.common gpf.pheno.db gpf.pheno.graphs gpf.pheno.import_tools gpf.pheno.pheno_data gpf.pheno.pheno_import gpf.pheno.prepare gpf.pheno.prepare.measure_classifier gpf.pheno.prepare_data gpf.pheno.registry gpf.pheno.storage gpf.pheno.update_pheno_descriptions gpf.pheno.utils gpf.pheno.utils.commons gpf.pheno.utils.lin_regress gpf.pheno_tool gpf.pheno_tool.pheno_tool_adapter gpf.pheno_tool.tool gpf.query_variants gpf.query_variants.attribute_queries gpf.query_variants.base_query_variants gpf.query_variants.query_runners gpf.query_variants.sql gpf.query_variants.sql.schema2 gpf.query_variants.sql.schema2.base_query_builder gpf.query_variants.sql.schema2.base_variants gpf.query_variants.sql.schema2.family_builder gpf.query_variants.sql.schema2.sql_query_builder gpf.query_variants.sql.schema2.summary_builder gpf.schema2_storage gpf.schema2_storage.schema2_import_storage gpf.schema2_storage.schema2_layout gpf.studies gpf.studies.study gpf.studies.variants_db gpf.testing gpf.testing.acgt_import gpf.testing.alla_import gpf.testing.foobar_import gpf.testing.import_helpers gpf.testing.setup_helpers gpf.testing.t4c8_import gpf.tools gpf.tools.dae2vcf gpf.tools.dataset_helpers gpf.tools.denovo2vcf gpf.tools.draw_pedigree gpf.tools.generate_common_report gpf.tools.generate_denovo_gene_sets gpf.tools.gpf_convert_study_config gpf.tools.gpf_validation_runner gpf.tools.grr_cache_repo gpf.tools.liftover_tools gpf.tools.ped2ped gpf.tools.reannotate_instance gpf.tools.simple_study_import gpf.tools.to_gpf_gene_models_format gpf.tools.vcf2tsv gpf.utils gpf.utils.testing gpf.utils.variant_utils gpf.variants gpf.variants.attributes gpf.variants.core gpf.variants.family_variant gpf.variants.variant gpf.variants_loaders gpf.variants_loaders.cnv gpf.variants_loaders.cnv.flexible_cnv_loader gpf.variants_loaders.cnv.loader gpf.variants_loaders.dae gpf.variants_loaders.dae.loader gpf.variants_loaders.parquet gpf.variants_loaders.parquet.loader gpf.variants_loaders.raw gpf.variants_loaders.raw.flexible_variant_loader gpf.variants_loaders.raw.loader gpf.variants_loaders.vcf gpf.variants_loaders.vcf.loader gpf.variants_loaders.vcf.serializer gpf_instance gpf_instance.apps gpf_instance.extension gpf_instance.gpf_instance gpf_instance.tests gpf_instance.tests.test_genome_view gpf_instance.tests.test_version_api gpf_web gpf_web.default_settings gpf_web.eager_settings gpf_web.gunicorn_settings gpf_web.mypy_settings gpf_web.remote_settings gpf_web.settings gpf_web.silk_settings gpf_web.wdaemanage gpf_web.wgpf gpf_web.wgpf_settings gpfjs gpfjs.views groups_api groups_api.migrations groups_api.tests measures_api measures_api.tests measures_api.tests.test_measures_api person_sets_api person_sets_api.tests person_sets_api.tests.test_person_sets_api pheno_browser_api pheno_browser_api.pheno_browser_helper pheno_browser_api.tests pheno_tool_api pheno_tool_api.adapter pheno_tool_api.tests pheno_tool_api.tests.test_pheno_tool_api query_base query_state_save query_state_save.migrations query_state_save.migrations.0001_initial query_state_save.migrations.0002_auto_20190205_0736 query_state_save.migrations.0003_querystate_origin_querystate_timestamp query_state_save.tests query_state_save.tests.conftest sentry sentry.tests sentry.tests.test_sentry sentry.urls sentry.views studies studies.conftest studies.query_transformer studies.response_transformer studies.study_wrapper studies.tests studies.tests.test_pheno_measures_columns studies.tests.test_query_transformer studies.tests.test_query_transformer_family_tags studies.tests.test_query_transformer_present_in_child_and_parent studies.tests.test_response_transformer_columns studies.tests.test_study_config_genotype_browser_columns studies.tests.test_study_group_person_sets_queries studies.tests.test_study_query_request studies.tests.test_study_wrapper studies.tests.test_study_wrapper_person_sets studies.tests.test_study_wrapper_queries studies.tests.test_study_wrapper_unique_variants_query user_queries user_queries.migrations user_queries.migrations.0001_initial users_api users_api.management users_api.management.commands users_api.management.commands.user_set_name users_api.management.commands.user_setpasswd users_api.management.commands.users_remove users_api.migrations users_api.migrations.0001_initial users_api.migrations.0002_auto_20190424_0751 users_api.migrations.0003_authenticationlog users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more users_api.migrations.0005_gpuserstate users_api.tests utils utils.authentication utils.datasets utils.email_regex utils.expand_gene_set utils.gene_sets utils.logger utils.pagination utils.password_requirements utils.query_params utils.streaming_response_util utils.testing

mom (gpf.variants.attributes.Role attribute) MULTIPLEX (gpf.pedigrees.family.FamilyTag attribute) MultiReader (class in gpf.parquet.schema2.loader)

N

name (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground property) (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentResourceBackground property) (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property) (gpf.enrichment_tool.samocha_background.SamochaEnrichmentBackground property) (gpf.gene_sets.denovo_gene_sets_config.EffectsCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.SexesCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.SingleCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.TripleCriteria attribute) (gpf.genomic_scores.scores.ScoreDesc attribute) (gpf.person_sets.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.person_sets.PersonSetConfig attribute) (gpf.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.PersonSetConfig attribute) (gpf.pheno.pheno_import.ImportInstrument attribute) (gpf.studies.study.GenotypeData property) (gpf_instance.apps.WDAEConfig attribute) (studies.study_wrapper.WDAEAbstractStudy property) name_in_gene_sets() (in module gene_sets.tests.test_gene_sets_api)

nan (gpf.pheno.prepare.measure_classifier.Convertible attribute) neg() (gpf.query_variants.attribute_queries.AttributeQueryTransformerFunction method) (gpf.query_variants.attribute_queries.AttributeQueryTransformerSQL method) (gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method) NO_RANK (gpf.pedigrees.pedigrees.Individual attribute) NOBODY_INTEREST_LOG_INTERVAL (gpf.query_variants.query_runners.QueryRunner attribute) NOBODY_INTEREST_THRESHOLD (gpf.query_variants.query_runners.QueryRunner attribute) non_numeric (gpf.pheno.prepare.measure_classifier.Convertible attribute) non_numeric_cutoff (gpf.pheno.common.InferenceConfig attribute) normalization_rules (gpf.configuration.gpf_config_parser.GPFConfigValidator attribute) normalize() (gpf.import_tools.import_tools.ImportConfigNormalizer method) not_role() (gpf.variants.attributes.Role static method) not_sequenced (gpf.pedigrees.family.Person property) NOTSET (gpf.tools.gpf_validation_runner.TestStatus attribute) NUCLEAR (gpf.pedigrees.family.FamilyTag attribute) number_config (gpf.pheno.common.MeasureHistogramConfigs attribute) number_of_children_with_event (gpf.common_reports.denovo_report.EffectCell property) number_of_observed_events (gpf.common_reports.denovo_report.EffectCell property) numeric (gpf.pheno.prepare.measure_classifier.Convertible attribute)

O

oauth_cookie_to_header() (in module utils.authentication) observed_rate_per_child (gpf.common_reports.denovo_report.EffectCell property) OffsetLayoutDrawer (class in gpf.pedigrees.drawing) omission (gpf.variants.attributes.Inheritance attribute) open() (gpf.variants_loaders.vcf.serializer.VcfSerializer method) open_file() (in module gpf.pheno.pheno_import) operations (datasets_api.migrations.0001_initial.Migration attribute) (datasets_api.migrations.0002_dataset_groups.Migration attribute) (datasets_api.migrations.0003_alter_dataset_options.Migration attribute) (datasets_api.migrations.0004_dataset_broken.Migration attribute) (datasets_api.migrations.0005_dataset_dataset_name.Migration attribute) (datasets_api.migrations.0006_datasethierarchy.Migration attribute) (datasets_api.migrations.0007_datasethierarchy_direct.Migration attribute) (datasets_api.migrations.0008_datasethierarchy_instance_id.Migration attribute) (query_state_save.migrations.0001_initial.Migration attribute) (query_state_save.migrations.0002_auto_20190205_0736.Migration attribute) (query_state_save.migrations.0003_querystate_origin_querystate_timestamp.Migration attribute) (user_queries.migrations.0001_initial.Migration attribute) (users_api.migrations.0001_initial.Migration attribute) (users_api.migrations.0002_auto_20190424_0751.Migration attribute) (users_api.migrations.0003_authenticationlog.Migration attribute) (users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more.Migration attribute) (users_api.migrations.0005_gpuserstate.Migration attribute)

OPTION (gpf.variants_loaders.raw.loader.ArgumentType attribute) or_() (gpf.query_variants.attribute_queries.AttributeQueryTransformerFunction method) (gpf.query_variants.attribute_queries.AttributeQueryTransformerSQL method) (gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method) ordinal (gpf.pheno.common.InferenceConfig attribute) (gpf.pheno.common.MeasureType attribute) other (gpf.pheno.common.MeasureType attribute) (gpf.variants.attributes.Inheritance attribute) other_parent() (gpf.pedigrees.pedigrees.MatingUnit method) overlap_enrichment_result_dict() (in module gpf.enrichment_tool.event_counters) overlap_event_counts() (in module gpf.enrichment_tool.event_counters)

P

PAGE_SIZE (gpf.gene_profile.db.GeneProfileDB attribute) (gpf.pheno.browser.PhenoBrowser attribute) page_size_query_param (utils.pagination.WdaePageNumberPagination attribute) paginate_queryset() (utils.pagination.WdaePageNumberPagination method) parent (gpf.variants.attributes.Role attribute) parents (gpf.studies.study.GenotypeData property) (studies.study_wrapper.WDAEAbstractStudy property) parents_id() (gpf.pedigrees.family_role_builder.Mating static method) parents_zygosity (gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute) ParquetGenotypeStorage (class in gpf.parquet_storage.storage) ParquetImportStorage (class in gpf.parquet_storage.storage) ParquetLoader (class in gpf.parquet.schema2.loader) (class in gpf.variants_loaders.parquet.loader) ParquetLoaderException ParquetLoaderVariants (class in gpf.parquet_storage.storage) parse() (gpf.parquet.partition_descriptor.PartitionDescriptor static method) (sentry.views.PlainTextParser method) parse_and_interpolate() (gpf.configuration.gpf_config_parser.GPFConfigParser static method) parse_and_interpolate_file() (gpf.configuration.gpf_config_parser.GPFConfigParser class method) parse_cli_argument() (gpf.variants_loaders.raw.loader.CLIArgument method) parse_cli_arguments() (gpf.pedigrees.loader.FamiliesLoader class method) (gpf.variants_loaders.cnv.loader.CNVLoader class method) (gpf.variants_loaders.dae.loader.DaeTransmittedLoader class method) (gpf.variants_loaders.dae.loader.DenovoLoader class method) (gpf.variants_loaders.raw.loader.CLILoader class method) (gpf.variants_loaders.vcf.loader.VcfLoader class method) (in module gpf.tools.dae2vcf) (in module gpf.tools.denovo2vcf) (in module gpf.tools.vcf2tsv) parse_denovo_gene_sets_config() (in module gpf.gene_sets.denovo_gene_sets_config) parse_denovo_gene_sets_study_config() (in module gpf.gene_sets.denovo_gene_sets_config) parse_dgsc_query() (in module gpf.gene_sets.denovo_gene_sets_config) parse_dict() (gpf.parquet.partition_descriptor.PartitionDescriptor static method) parse_duckdb_config() (in module gpf.duckdb_storage.duckdb_storage_config) parse_person_set_collection_config() (in module gpf.person_sets) (in module gpf.person_sets.person_sets) parse_person_set_collections_study_config() (in module gpf.person_sets) (in module gpf.person_sets.person_sets) parse_person_set_config() (in module gpf.person_sets) (in module gpf.person_sets.person_sets) parse_query_params() (in module utils.query_params) parse_recurrency_criteria() (in module gpf.gene_sets.denovo_gene_sets_config) parse_string() (gpf.parquet.partition_descriptor.PartitionDescriptor static method) Partition (class in gpf.parquet.partition_descriptor) partition_directory() (gpf.parquet.partition_descriptor.PartitionDescriptor static method) partition_filename() (gpf.parquet.partition_descriptor.PartitionDescriptor static method) PartitionDescriptor (class in gpf.parquet.partition_descriptor) PASSED (gpf.tools.gpf_validation_runner.TestStatus attribute) passed_case_count (gpf.tools.gpf_validation_runner.AbstractRunner property) (gpf.tools.gpf_validation_runner.MainRunner property) paternal_aunt (gpf.variants.attributes.Role attribute) paternal_cousin (gpf.variants.attributes.Role attribute) paternal_grandfather (gpf.variants.attributes.Role attribute) paternal_grandmother (gpf.variants.attributes.Role attribute) paternal_half_sibling (gpf.variants.attributes.Role attribute) paternal_uncle (gpf.variants.attributes.Role attribute) path (gpf.pheno.common.DataDictionaryConfig attribute) (gpf.pheno.common.GPFInstanceConfig attribute) (gpf.pheno.common.InstrumentConfig attribute) (gpf.pheno.common.InstrumentDictionaryConfig attribute) path_to_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor static method) PDFLayoutDrawer (class in gpf.pedigrees.drawing) ped_1() (in module enrichment_api.tests.test_t4c8_enrichment) ped_df (gpf.pedigrees.families_data.FamiliesData property) pedigree (gpf.pheno.common.PhenoImportConfig attribute) (gpf.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute) (gpf.schema2_storage.schema2_layout.Schema2DatasetLayout attribute) (gpf.testing.import_helpers.StudyInputLayout attribute) pedigree_import() (in module gpf.testing.import_helpers) pedigree_parquet_schema() (in module gpf.parquet.parquet_writer) pedigree_samples() (gpf.pedigrees.families_data.FamiliesData method) PeopleCounter (class in gpf.common_reports.people_counter) PeopleCounters (class in gpf.common_reports.people_counter) PeopleReport (class in gpf.common_reports.people_counter) percent_of_children_with_events (gpf.common_reports.denovo_report.EffectCell property) Person (class in gpf.pedigrees.family) person_column (gpf.pheno.common.InstrumentConfig attribute) (gpf.pheno.common.PhenoImportConfig attribute) (gpf.pheno.pheno_import.ImportInstrument attribute) person_ids (gpf.studies.study.PSCQueryAdjustments attribute) person_ids() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) person_set_collections (gpf.pheno.common.StudyConfig attribute) (gpf.pheno.pheno_data.PhenotypeData property) (gpf.pheno.pheno_data.PhenotypeGroup property) (gpf.pheno.pheno_data.PhenotypeStudy property) (gpf.studies.study.GenotypeData property) (studies.study_wrapper.WDAEAbstractStudy property) person_sets_api module person_sets_api.tests module person_sets_api.tests.test_person_sets_api module PersonFilter (class in gpf.person_filters) (class in gpf.person_filters.person_filters) PersonFilterRange (class in gpf.person_filters) (class in gpf.person_filters.person_filters)

PersonFilterSet (class in gpf.person_filters) (class in gpf.person_filters.person_filters) persons (gpf.enrichment_tool.genotype_helper.AlleleEvent attribute) persons_with_parent() (gpf.pedigrees.families_data.FamiliesData method) persons_with_parents() (gpf.pedigrees.families_data.FamiliesData method) persons_without_parents() (gpf.pedigrees.families_data.FamiliesData method) PersonSet (class in gpf.person_sets) (class in gpf.person_sets.person_sets) PersonSetCollection (class in gpf.person_sets) (class in gpf.person_sets.person_sets) PersonSetCollectionConfig (class in gpf.person_sets) (class in gpf.person_sets.person_sets) PersonSetConfig (class in gpf.person_sets) (class in gpf.person_sets.person_sets) pheno_browser_api module pheno_browser_api.pheno_browser_helper module pheno_browser_api.tests module pheno_cli_parser() (in module gpf.pheno.build_pheno_browser) (in module gpf.pheno.import_tools) (in module gpf.pheno.pheno_import) (in module gpf.pheno.update_pheno_descriptions) pheno_id (gpf.pheno.pheno_data.PhenotypeData property) pheno_tool_api module pheno_tool_api.adapter module pheno_tool_api.tests module pheno_tool_api.tests.test_pheno_tool_api module PhenoBrowser (class in gpf.pheno.browser) PhenoBrowserHelper (class in pheno_browser_api.pheno_browser_helper) PhenoDb (class in gpf.pheno.db) PhenoFilter (class in gpf.person_filters) (class in gpf.person_filters.person_filters) PhenoFilterRange (class in gpf.person_filters) (class in gpf.person_filters.person_filters) PhenoFilterSet (class in gpf.person_filters) (class in gpf.person_filters.person_filters) PhenoImportConfig (class in gpf.pheno.common) PhenoRegistry (class in gpf.pheno.registry) PhenoResult (class in gpf.pheno_tool.tool) PhenoTool (class in gpf.pheno_tool.tool) PhenoToolAdapter (class in gpf.pheno_tool.pheno_tool_adapter) (class in pheno_tool_api.adapter) PhenoToolAdapterBase (class in gpf.pheno_tool.pheno_tool_adapter) (class in pheno_tool_api.adapter) PhenoToolHelper (class in gpf.pheno_tool.tool) phenotype (gpf.studies.study.GenotypeData property) PHENOTYPE_ATTRS (studies.response_transformer.ResponseTransformer attribute) phenotype_data (studies.study_wrapper.WDAEAbstractStudy property) phenotype_person_sets() (in module studies.tests.test_response_transformer_columns) phenotype_storages (gpf.gpf_instance.gpf_instance.GPFInstance property) (gpf.gpf_instance.GPFInstance property) PhenotypeData (class in gpf.pheno.pheno_data) PhenotypeGroup (class in gpf.pheno.pheno_data) PhenotypeStorage (class in gpf.pheno.storage) PhenotypeStorageRegistry (class in gpf.pheno.storage) PhenotypeStudy (class in gpf.pheno.pheno_data) PlainTextParser (class in sentry.views) Point (class in gpf.pedigrees.layout) poisson_test() (in module gpf.enrichment_tool.samocha_background) position (gpf.variants.core.Allele property) (gpf.variants.core.Allele.Type attribute) (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) (gpf.variants.variant.SummaryVariant property) possible_denovo (gpf.variants.attributes.Inheritance attribute) possible_omission (gpf.variants.attributes.Inheritance attribute) prb (gpf.variants.attributes.Role attribute) PreparePhenoBrowserBase (class in gpf.pheno.prepare_data) preview_sources() (in module genotype_browser.tests.conftest) process_config() (gpf.configuration.gpf_config_parser.GPFConfigParser static method) process_config_raw() (gpf.configuration.gpf_config_parser.GPFConfigParser static method) process_parquet() (in module gpf.parquet.schema2.annotate_schema2_parquet) process_region() (in module gpf.gene_profile.generate_gene_profile) produce_download() (pheno_tool_api.adapter.PhenoToolAdapter method) (pheno_tool_api.adapter.PhenoToolAdapterBase method) produce_genotype() (gpf.variants_loaders.dae.loader.DenovoLoader static method) produce_regions() (in module gpf.parquet.schema2.annotate_schema2_parquet) produce_schema2_annotation_tasks() (in module gpf.parquet.schema2.annotate_schema2_parquet) produce_schema2_merging_tasks() (in module gpf.parquet.schema2.annotate_schema2_parquet) psc_config() (in module enrichment_api.tests.conftest) psc_id (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (gpf.person_sets.person_sets.PSCQuery attribute) (gpf.person_sets.PSCQuery attribute) PSCQuery (class in gpf.person_sets) (class in gpf.person_sets.person_sets) PSCQueryAdjustments (class in gpf.studies.study) pseudo_autosomal (gpf.variants.attributes.GeneticModel attribute) pub_med (gpf.studies.study.GenotypeData property) put_value_in_result_queue() (gpf.query_variants.query_runners.QueryRunner method) pvalues (gpf.pheno.utils.lin_regress.LinearRegression property)

Q

QUAD (gpf.pedigrees.family.FamilyTag attribute) query_base module query_fpids() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) query_gp_statistics() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) query_gps() (gpf.gene_profile.db.GeneProfileDB method) query_load() (in module query_state_save.tests.conftest) query_person_ids() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) query_save() (in module query_state_save.tests.conftest) query_state_save module query_state_save.migrations module query_state_save.migrations.0001_initial module query_state_save.migrations.0002_auto_20190205_0736 module query_state_save.migrations.0003_querystate_origin_querystate_timestamp module query_state_save.tests module query_state_save.tests.conftest module

query_summary_variants() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) (gpf.parquet_storage.storage.ParquetLoaderVariants method) (gpf.studies.study.GenotypeData method) query_transformer() (in module studies.tests.test_study_group_person_sets_queries) (in module studies.tests.test_study_wrapper_person_sets) (in module studies.tests.test_study_wrapper_unique_variants_query) query_variants() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) (gpf.parquet_storage.storage.ParquetLoaderVariants method) (gpf.studies.study.GenotypeData method) query_variants_download_wdae() (studies.study_wrapper.WDAEAbstractStudy method) (studies.study_wrapper.WDAEStudy method) query_variants_preview_wdae() (studies.study_wrapper.WDAEAbstractStudy method) (studies.study_wrapper.WDAEStudy method) query_variants_raw() (studies.study_wrapper.WDAEStudy method) query_variants_wdae() (studies.study_wrapper.WDAEAbstractStudy method) (studies.study_wrapper.WDAEStudy method) QueryBuilderBase (class in gpf.query_variants.sql.schema2.sql_query_builder) QueryCompoundAdditionTransformer (class in gpf.query_variants.attribute_queries) QueryHeuristics (class in gpf.query_variants.sql.schema2.sql_query_builder) QueryResult (class in gpf.query_variants.query_runners) QueryRunner (class in gpf.query_variants.query_runners) QueryTransformer (class in studies.query_transformer) QueryTransformerProtocol (class in studies.study_wrapper) QueryVariants (class in gpf.query_variants.base_query_variants) QueryVariantsBase (class in gpf.query_variants.base_query_variants) QUOTE (gpf.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute)

R

RankRange (class in gpf.pheno.common) raw (gpf.pheno.common.MeasureType attribute) RawFamilyVariants (class in gpf.inmemory_storage.raw_variants) RawMemoryVariants (class in gpf.inmemory_storage.raw_variants) RawVariantsQueryRunner (class in gpf.inmemory_storage.raw_variants) read_and_classify_measure() (in module gpf.pheno.pheno_import) read_instrument_measure_names() (in module gpf.pheno.pheno_import) read_only (gpf.duckdb_storage.duckdb_storage_config.DuckDbConf attribute) (gpf.genotype_storage.genotype_storage.GenotypeStorage property) read_pedigree() (in module gpf.pheno.pheno_import) Reader (class in gpf.parquet.schema2.loader) ReadOnlyDBAuthentication (class in utils.authentication) ready() (gpf_instance.apps.WDAEConfig method) real_attr() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) real_persons (gpf.pedigrees.families_data.FamiliesData property) Realization (class in gpf.pedigrees.pedigrees) ReannotateInstanceTool (class in gpf.tools.reannotate_instance) rebuild_families() (gpf.studies.study.GenotypeDataGroup method) rec (gpf.enrichment_tool.event_counters.EnrichmentResult attribute) (gpf.enrichment_tool.event_counters.EventCountersResult attribute) (gpf.enrichment_tool.event_counters.EventsResult attribute) (gpf.enrichment_tool.event_counters.VariantEventsResult attribute) rec_genes (gpf.enrichment_tool.event_counters.EnrichmentResult attribute) (gpf.enrichment_tool.event_counters.EventCountersResult attribute) recurrency (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) RecurrentCriteria (class in gpf.gene_sets.denovo_gene_sets_config) red (gpf_web.default_settings.CustomFormatter attribute) redefine() (gpf.pedigrees.families_data.FamiliesData method) (gpf.pedigrees.family.Family method) (gpf.pedigrees.family.Person method) ref_allele (gpf.variants.variant.SummaryVariant property) reference (gpf.variants.attributes.Inheritance attribute) (gpf.variants.core.Allele property) (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) (gpf.variants.variant.SummaryVariant property) reference_genome (gpf.gpf_instance.gpf_instance.GPFInstance property) (gpf.gpf_instance.GPFInstance property) reference_genotype() (in module gpf.utils.variant_utils) region_bin (gpf.import_tools.import_tools.Bucket attribute) (gpf.parquet.partition_descriptor.Partition attribute) region_bins (gpf.query_variants.sql.schema2.sql_query_builder.QueryHeuristics attribute) region_bins() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) region_bins_count() (gpf.parquet.partition_descriptor.PartitionDescriptor method) REGION_BINS_HEURISTIC_CUTOFF (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase attribute) region_to_region_bins() (gpf.parquet.partition_descriptor.PartitionDescriptor method) regions (gpf.import_tools.import_tools.Bucket attribute) regions() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) register_default_storage() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) (gpf.pheno.storage.PhenotypeStorageRegistry method) register_genotype_data() (gpf.studies.variants_db.VariantsDb method) register_genotype_storage() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) register_genotype_storage_factory() (in module gpf.genotype_storage.genotype_storage_registry) register_import_storage_factory() (in module gpf.import_tools.import_tools) register_phenotype_data() (gpf.pheno.registry.PhenoRegistry method)

register_phenotype_storage() (gpf.pheno.storage.PhenotypeStorageRegistry method) register_storage_config() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) (gpf.pheno.storage.PhenotypeStorageRegistry method) register_storages_configs() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) (gpf.pheno.storage.PhenotypeStorageRegistry method) regression_display_names (gpf.pheno.browser.PhenoBrowser property) regression_display_names_with_ids (gpf.pheno.browser.PhenoBrowser property) regression_ids (gpf.pheno.browser.PhenoBrowser property) RegressionMeasure (class in gpf.pheno.common) regressions (gpf.pheno.common.StudyConfig attribute) reload() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) (gpf.studies.variants_db.VariantsDb method) remove_annoying_characters() (in module gpf.pheno.utils.commons) remove_elements() (gpf.common_reports.denovo_report.EffectRow method) remove_empty_person_sets() (gpf.person_sets.person_sets.PersonSetCollection static method) (gpf.person_sets.PersonSetCollection static method) remove_none_values() (in module studies.study_wrapper) remove_study_config() (gpf.tools.dataset_helpers.DatasetHelpers method) rename_study_config() (gpf.tools.dataset_helpers.DatasetHelpers method) replace_tables() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) report_variant() (gpf.tools.liftover_tools.VCFLiftoverTool static method) report_vcf_variant() (gpf.tools.liftover_tools.VCFLiftoverTool static method) request_logging() (in module utils.logger) request_logging_function_view() (in module utils.logger) reset (gpf_web.default_settings.CustomFormatter attribute) reset_regions() (gpf.variants_loaders.raw.loader.VariantsGenotypesLoader method) (gpf.variants_loaders.raw.loader.VariantsLoader method) (gpf.variants_loaders.vcf.loader.VcfLoader method) resolve_tags() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) resource_id (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground property) (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property) (gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation property) (gpf.genomic_scores.scores.ScoreDesc attribute) response_transformer() (in module studies.tests.test_study_group_person_sets_queries) ResponseTransformer (class in studies.response_transformer) ResponseTransformerProtocol (class in studies.study_wrapper) result_queue (gpf.query_variants.query_runners.QueryRunner property) Role (class in gpf.variants.attributes) role (gpf.pedigrees.family.Person property) role_labels() (in module gpf.pheno.graphs) roles (gpf.studies.study.PSCQueryAdjustments attribute) roles() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) rules (gpf.configuration.gpf_config_parser.GPFConfigValidator attribute) run() (gpf.duckdb_storage.duckdb2_variants.DuckDb2Runner method) (gpf.duckdb_storage.duckdb_variants.DuckDbRunner method) (gpf.inmemory_storage.raw_variants.RawVariantsQueryRunner method) (gpf.pheno.prepare_data.PreparePhenoBrowserBase method) (gpf.query_variants.query_runners.QueryRunner method) (gpf.tools.gpf_validation_runner.GenotypeBrowserRunner method) (gpf.tools.liftover_tools.LiftoverTool method) (gpf.tools.reannotate_instance.ReannotateInstanceTool method) run_with_project() (in module gpf.import_tools.cli) RUNNER_CLASS (gpf.duckdb_storage.duckdb_variants.DuckDbVariants attribute) (gpf.query_variants.base_query_variants.QueryVariantsBase attribute) (gpf.query_variants.sql.schema2.base_variants.SqlSchema2Variants attribute)

S

safe_db_name() (in module gpf.pheno.db) samocha_background() (in module enrichment_api.tests.conftest) SamochaEnrichmentBackground (class in gpf.enrichment_tool.samocha_background) sample_index (gpf.pedigrees.family.Person property) samples_index (gpf.pedigrees.family.Family property) SandwichInstance (class in gpf.pedigrees.pedigrees) SandwichSolver (class in gpf.pedigrees.pedigrees) save() (gpf.common_reports.common_report.CommonReport method) (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) (gpf.pheno.browser.PhenoBrowser method) save_descriptions() (gpf.pheno.browser.PhenoBrowser method) (gpf.pheno.db.PhenoDb method) (in module gpf.pheno.update_pheno_descriptions) save_families() (gpf.pedigrees.loader.FamiliesLoader static method) save_fig() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method) save_object() (in module query_state_save.tests.conftest) save_ped_df_to_parquet() (in module gpf.parquet.parquet_writer) save_pedigree() (gpf.pedigrees.loader.FamiliesLoader static method) save_regression() (gpf.pheno.browser.PhenoBrowser method) save_regression_values() (gpf.pheno.browser.PhenoBrowser method) save_study_config() (in module gpf.import_tools.import_tools) scale() (gpf.pedigrees.layout.Layout method) schema() (gpf.parquet.schema2.serializers.AlleleParquetSerializer method) (gpf.parquet.schema2.serializers.FamilyAlleleParquetSerializer method) (gpf.parquet.schema2.serializers.SummaryAlleleParquetSerializer method) schema1_partition() (gpf.parquet.partition_descriptor.PartitionDescriptor method) schema2_project_dataset_layout() (in module gpf.schema2_storage.schema2_import_storage) Schema2DatasetLayout (class in gpf.schema2_storage.schema2_layout) Schema2ImportStorage (class in gpf.schema2_storage.schema2_import_storage) Schema2SummaryVariantBatchConsumer (class in gpf.parquet.schema2.variants_parquet_writer) Schema2SummaryVariantConsumer (class in gpf.parquet.schema2.variants_parquet_writer) Schema2SummaryVariantsBatchSource (class in gpf.parquet.schema2.processing_pipeline) Schema2SummaryVariantsSource (class in gpf.parquet.schema2.processing_pipeline) Schema2VariantBatchConsumer (class in gpf.parquet.schema2.variants_parquet_writer) Schema2VariantConsumer (class in gpf.parquet.schema2.variants_parquet_writer) score_id (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property) ScoreDesc (class in gpf.genomic_scores.scores) search_measures() (gpf.pheno.browser.PhenoBrowser method) (gpf.pheno.pheno_data.PhenotypeData method) (pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method) (pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method) select_events_in_person_set() (gpf.enrichment_tool.event_counters.CounterBase method) selected_family_tags (gpf.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute) selected_person_set_collections (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) selected_person_sets (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (gpf.person_sets.person_sets.PSCQuery attribute) (gpf.person_sets.PSCQuery attribute) sentry module sentry() (in module sentry.views) sentry.tests module sentry.tests.test_sentry module sentry.urls module sentry.views module serialize() (enrichment_api.enrichment_serializer.EnrichmentSerializer method) (gpf.parquet.partition_descriptor.PartitionDescriptor method) (gpf.variants_loaders.vcf.serializer.VcfSerializer method) serialize_all() (enrichment_api.enrichment_serializer.EnrichmentSerializer method) serialize_common_filter() (enrichment_api.enrichment_serializer.EnrichmentSerializer method) serialize_enrichment_result() (enrichment_api.enrichment_serializer.EnrichmentSerializer method) serialize_family() (gpf.parquet.schema2.serializers.JsonVariantsDataSerializer method) (gpf.parquet.schema2.serializers.VariantsDataSerializer method) serialize_female() (enrichment_api.enrichment_serializer.EnrichmentSerializer method) serialize_full_variant() (gpf.variants_loaders.vcf.serializer.VcfSerializer method) serialize_male() (enrichment_api.enrichment_serializer.EnrichmentSerializer method) serialize_overlap_filter() (enrichment_api.enrichment_serializer.EnrichmentSerializer method) serialize_people_groups() (enrichment_api.enrichment_serializer.EnrichmentSerializer method) serialize_rec() (enrichment_api.enrichment_serializer.EnrichmentSerializer method) serialize_rec_filter() (enrichment_api.enrichment_serializer.EnrichmentSerializer method) serialize_summary() (gpf.parquet.schema2.serializers.JsonVariantsDataSerializer method) (gpf.parquet.schema2.serializers.VariantsDataSerializer method) serialize_summary_schema() (in module gpf.parquet.parquet_writer) SessionAuthenticationWithoutCSRF (class in utils.authentication) SessionAuthenticationWithUnauthenticatedCSRF (class in utils.authentication) set_attr() (gpf.pedigrees.family.Person method) (in module gpf.pedigrees.family_tag_builder) set_attribute() (gpf.variants_loaders.raw.loader.VariantsLoader method) set_figure_size() (in module gpf.pheno.graphs) set_fit_request() (gpf.pheno.utils.lin_regress.LinearRegression method) set_matched_alleles() (gpf.variants.variant.SummaryVariant method) set_negative_stats() (gpf.pheno_tool.tool.PhenoResult method) set_positive_stats() (gpf.pheno_tool.tool.PhenoResult method) set_result_queue() (gpf.query_variants.query_runners.QueryRunner method) set_score_request() (gpf.pheno.utils.lin_regress.LinearRegression method) set_study_id() (gpf.query_variants.query_runners.QueryRunner method) set_tag() (gpf.pedigrees.family.Family method) (gpf.pedigrees.family.Person method) (in module gpf.pedigrees.family_tag_builder) setup() (gpf_instance.extension.GPFExtensionBase method) setup_dataset() (in module gpf.testing.import_helpers) setup_dataset_config() (in module gpf.testing.import_helpers) setup_gpf_instance() (in module gpf.testing.setup_helpers) setup_import_project() (in module gpf.testing.import_helpers) setup_import_project_config() (in module gpf.testing.import_helpers) setup_t4c8_grr() (in module utils.testing) setup_t4c8_instance() (in module gpf.utils.testing) (in module utils.testing) setup_wgpf_instance() (in module utils.testing) Sex (class in gpf.variants.attributes) sex (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (gpf.pedigrees.family.Person property) sex_zygosity (gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute) sexes (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) (gpf.gene_sets.denovo_gene_sets_config.SexesCriteria attribute) (gpf.studies.study.PSCQueryAdjustments attribute) sexes() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) SexesCriteria (class in gpf.gene_sets.denovo_gene_sets_config) short() (gpf.variants.attributes.Sex method) (gpf.variants.attributes.Status method) shutdown() (gpf.duckdb_storage.duckdb_genotype_storage.AbstractDuckDbStorage method) (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) (gpf.genotype_storage.genotype_storage.GenotypeStorage method) (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) (gpf.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage method) (gpf.parquet_storage.storage.ParquetGenotypeStorage method) (gpf.pheno.registry.PhenoRegistry method) (gpf.pheno.storage.PhenotypeStorage method) (gpf.pheno.storage.PhenotypeStorageRegistry method) sib (gpf.variants.attributes.Role attribute) SibshipUnit (class in gpf.pedigrees.pedigrees) simple_query_data() (in module query_state_save.tests.conftest) SIMPLEX (gpf.pedigrees.family.FamilyTag attribute) SingleCriteria (class in gpf.gene_sets.denovo_gene_sets_config) SingleVcfLoader (class in gpf.variants_loaders.vcf.loader) SIZE (gpf.pedigrees.layout.IndividualWithCoordinates attribute) size() (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) (gpf.parquet.schema2.variants_parquet_writer.ContinuousParquetFileWriter method) skip (gpf.pheno.common.InferenceConfig attribute) skip_pedigree_measures (gpf.pheno.common.PhenoImportConfig attribute) skipped (gpf.pheno.common.MeasureType attribute) small_deletion (gpf.variants.core.Allele.Type attribute) SMALL_DPI (gpf.pheno.prepare_data.PreparePhenoBrowserBase attribute) small_insertion (gpf.variants.core.Allele.Type attribute)

small_values_desc (gpf.genomic_scores.scores.ScoreDesc attribute) solve() (gpf.pedigrees.pedigrees.SandwichSolver static method) source (gpf.genomic_scores.scores.ScoreDesc attribute) (gpf.person_sets.person_sets.SourceConfig attribute) (gpf.person_sets.SourceConfig attribute) SourceConfig (class in gpf.person_sets) (class in gpf.person_sets.person_sets) sources (gpf.person_sets.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.PersonSetCollectionConfig attribute) SPECIAL_ATTRS (studies.response_transformer.ResponseTransformer attribute) split_events() (gpf.enrichment_tool.event_counters.CounterBase method) split_heuristics() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) split_location() (gpf.variants_loaders.dae.loader.DenovoLoader static method) spouse (gpf.variants.attributes.Role attribute) SqlQueryBuilder (class in gpf.query_variants.sql.schema2.sql_query_builder) SqlSchema2Variants (class in gpf.query_variants.sql.schema2.base_variants) start (gpf.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.SingleCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.TripleCriteria attribute) start() (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbParquetStorage method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3ParquetStorage method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3Storage method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbStorage method) (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) (gpf.genotype_storage.genotype_storage.GenotypeStorage method) (gpf.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage method) (gpf.parquet_storage.storage.ParquetGenotypeStorage method) (gpf.query_variants.query_runners.QueryResult method) (gpf.query_variants.query_runners.QueryRunner method) Status (class in gpf.variants.attributes) status (gpf.pedigrees.family.Person property) status_zygosity (gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute) statuses() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) step_dad (gpf.variants.attributes.Role attribute) step_mom (gpf.variants.attributes.Role attribute) storage_dir (gpf.pheno.common.DestinationConfig attribute) storage_id (gpf.pheno.common.DestinationConfig attribute) storage_type (gpf.duckdb_storage.duckdb_storage_config.DuckDbConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbParquetConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute) store_junit_results() (gpf.tools.gpf_validation_runner.MainRunner static method) store_results() (gpf.tools.gpf_validation_runner.GenotypeBrowserRunner method) (gpf.tools.gpf_validation_runner.MainRunner method) str2fgt() (in module gpf.utils.variant_utils) str2gt() (in module gpf.utils.variant_utils) str2lists() (in module gpf.utils.variant_utils) str2mat() (in module gpf.utils.variant_utils) str2mat_adjust_colsep() (in module gpf.utils.variant_utils) STREAMING_CHUNK_SIZE (studies.response_transformer.ResponseTransformer attribute) string_type() (gpf.query_variants.sql.schema2.base_query_builder.Dialect static method) studies module studies.conftest module studies.query_transformer module studies.response_transformer module studies.study_wrapper module studies.tests module studies.tests.test_pheno_measures_columns module studies.tests.test_query_transformer module studies.tests.test_query_transformer_family_tags module studies.tests.test_query_transformer_present_in_child_and_parent module studies.tests.test_response_transformer_columns module studies.tests.test_study_config_genotype_browser_columns module studies.tests.test_study_group_person_sets_queries module studies.tests.test_study_query_request module studies.tests.test_study_wrapper module studies.tests.test_study_wrapper_person_sets module studies.tests.test_study_wrapper_queries module studies.tests.test_study_wrapper_unique_variants_query module study (gpf.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute) (gpf.schema2_storage.schema2_layout.Schema2DatasetLayout attribute) study_1() (in module enrichment_api.tests.test_t4c8_enrichment) (in module studies.tests.test_study_group_person_sets_queries) study_2() (in module studies.tests.test_study_group_person_sets_queries) study_config (gpf.pheno.common.PhenoImportConfig attribute) study_configs (gpf.genotype_storage.genotype_storage.GenotypeStorage property) study_data() (in module enrichment_api.tests.conftest) study_id (gpf.import_tools.import_tools.ImportProject property) (gpf.studies.study.GenotypeData property) (gpf.testing.import_helpers.StudyInputLayout attribute) (studies.study_wrapper.WDAEAbstractStudy property) study_phenotype (gpf.studies.study.GenotypeDataStudy property) study_type (gpf.studies.study.GenotypeData property) study_update() (in module gpf.testing.import_helpers) StudyConfig (class in gpf.pheno.common) StudyConfigBuilder (class in gpf.configuration.study_config_builder) StudyConfigsAdjustmentCommand (class in gpf.gpf_instance.adjustments.gpf_instance_adjustments) StudyInputLayout (class in gpf.testing.import_helpers) substitution (gpf.variants.core.Allele.Type attribute) summary (gpf.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute) (gpf.schema2_storage.schema2_layout.Schema2DatasetLayout attribute) summary() (gpf.tools.gpf_validation_runner.MainRunner method) summary_allele (gpf.variants.family_variant.FamilyAllele attribute) summary_allele_from_record() (gpf.variants.variant.SummaryVariantFactory static method) summary_attributes (gpf.variants.family_variant.FamilyAllele property) summary_base() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) SUMMARY_COLUMNS (gpf.parquet.schema2.loader.ParquetLoader attribute) summary_download_sources() (in module genotype_browser.tests.conftest) summary_index (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) (gpf.variants.variant.SummaryAllele property) (gpf.variants.variant.SummaryVariant property) summary_partition() (gpf.parquet.partition_descriptor.PartitionDescriptor method) summary_partition_schema() (gpf.parquet.partition_descriptor.PartitionDescriptor method) summary_preview_sources() (in module genotype_browser.tests.conftest) summary_query() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) summary_variant (gpf.variants_loaders.raw.loader.FullVariant attribute) summary_variant_filter_function() (gpf.inmemory_storage.raw_variants.RawFamilyVariants class method) summary_variant_from_records() (gpf.variants.variant.SummaryVariantFactory static method) summary_variant_from_vcf() (gpf.variants.variant.SummaryVariantFactory static method) summary_variants() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) summary_variants_iterator() (gpf.inmemory_storage.raw_variants.RawFamilyVariants method) SummaryAllele (class in gpf.variants.variant) SummaryAlleleParquetSerializer (class in gpf.parquet.schema2.serializers) SummaryQueryBuilder (class in gpf.query_variants.sql.schema2.summary_builder) SummaryVariant (class in gpf.variants.variant) SummaryVariantFactory (class in gpf.variants.variant) svuid (gpf.variants.variant.SummaryVariant property) symlink_pedigree_and_family_variants() (in module gpf.parquet.schema2.annotate_schema2_parquet) SyntaxSugarTransformer (class in gpf.query_variants.attribute_queries)

T

t4c8_fixture() (in module enrichment_api.tests.conftest) t4c8_gpf() (in module gpf.testing.t4c8_import) tag_affected_dad_family() (in module gpf.pedigrees.family_tag_builder) tag_affected_mom_family() (in module gpf.pedigrees.family_tag_builder) tag_affected_prb_family() (in module gpf.pedigrees.family_tag_builder) tag_affected_sib_family() (in module gpf.pedigrees.family_tag_builder) tag_control_family() (in module gpf.pedigrees.family_tag_builder) tag_families_data() (in module gpf.pedigrees.families_data) tag_family() (gpf.pedigrees.family_tag_builder.FamilyTagsBuilder method) tag_family_type() (gpf.pedigrees.family_tag_builder.FamilyTagsBuilder method) tag_female_prb_family() (in module gpf.pedigrees.family_tag_builder) tag_labels (gpf.pedigrees.family.Family property) tag_male_prb_family() (in module gpf.pedigrees.family_tag_builder) tag_missing_dad_family() (in module gpf.pedigrees.family_tag_builder) tag_missing_mom_family() (in module gpf.pedigrees.family_tag_builder) tag_multiplex_family() (in module gpf.pedigrees.family_tag_builder) tag_nuclear_family() (in module gpf.pedigrees.family_tag_builder) tag_quad_family() (in module gpf.pedigrees.family_tag_builder) tag_simplex_family() (in module gpf.pedigrees.family_tag_builder) tag_trio_family() (in module gpf.pedigrees.family_tag_builder) tag_unaffected_dad_family() (in module gpf.pedigrees.family_tag_builder) tag_unaffected_mom_family() (in module gpf.pedigrees.family_tag_builder) tag_unaffected_prb_family() (in module gpf.pedigrees.family_tag_builder) tag_unaffected_sib_family() (in module gpf.pedigrees.family_tag_builder) tags (gpf.pedigrees.family.Family property) (gpf.pedigrees.family.Person property) TAGS (gpf.pedigrees.family_tag_builder.FamilyTagsBuilder attribute) tags_or_mode (gpf.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute) tags_to_family_ids() (gpf.query_variants.base_query_variants.QueryVariants method) TagsQuery (class in gpf.query_variants.sql.schema2.sql_query_builder) tandem_repeat (gpf.variants.core.Allele.Type attribute) tandem_repeat() (in module gpf.variants.variant) tandem_repeat_del (gpf.variants.core.Allele.Type attribute) tandem_repeat_ins (gpf.variants.core.Allele.Type attribute) test_affected_status() (in module studies.tests.test_query_transformer) test_attributes_query_roles() (in module studies.tests.test_query_transformer_present_in_child_and_parent) test_autogenerate_common_report() (in module common_reports_api.tests.test_common_reports_api) test_bad_gene_score_partition() (in module gene_scores.tests.test_scores_partitions) test_bad_gene_set_collection_not_found() (in module gene_sets.tests.test_gene_sets_api) test_build() (in module enrichment_api.tests.test_enrichment_builder) test_build_people_group_selector() (in module enrichment_api.tests.test_enrichment_builder) test_build_results() (in module enrichment_api.tests.test_enrichment_builder) test_build_study_1_enrichment_cache() (in module enrichment_api.tests.test_t4c8_enrichment) test_collection_configs_view() (in module person_sets_api.tests.test_person_sets_api) test_collection_domain_view() (in module person_sets_api.tests.test_person_sets_api) test_configuration() (in module gene_profiles_api.tests.test_agp_api) (in module gene_profiles_api.tests.test_agp_api_configless) test_dataset_person_sets_queries() (in module studies.tests.test_study_group_person_sets_queries) test_dataset_simple() (in module studies.tests.test_study_group_person_sets_queries) test_default_gene_models_id() (in module genomes_api.tests.test_gene_models_api) test_denovo_gene_set_download() (in module gene_sets.tests.test_gene_sets_api) test_denovo_gene_set_not_found() (in module gene_sets.tests.test_gene_sets_api) test_denovo_gene_sets() (in module gene_sets.tests.test_gene_sets_api) test_denovo_gene_sets_types() (in module gene_sets.tests.test_gene_sets_api) test_effect_details_download() (in module genotype_browser.tests.test_effect_types_download) test_enrichment_api_permissions() (in module enrichment_api.tests.test_enrichment_api) test_enrichment_models() (in module enrichment_api.tests.test_enrichment_api) test_enrichment_models_missing_study() (in module enrichment_api.tests.test_enrichment_api) test_enrichment_test_missing_dataset_id() (in module enrichment_api.tests.test_enrichment_api) test_enrichment_test_missing_gene_symbols() (in module enrichment_api.tests.test_enrichment_api) test_enrichment_test_missing_study() (in module enrichment_api.tests.test_enrichment_api) test_enrichment_test_with_gene_score() (in module enrichment_api.tests.test_enrichment_api) test_enrichment_test_with_gene_score_with_zero_range() (in module enrichment_api.tests.test_enrichment_api) test_enrichment_test_with_gene_set() (in module enrichment_api.tests.test_enrichment_api) test_enrichment_test_with_gene_symbols() (in module enrichment_api.tests.test_enrichment_api) test_families_data_all_download() (in module common_reports_api.tests.test_common_reports_api) test_families_data_all_download_no_permissions() (in module common_reports_api.tests.test_common_reports_api) test_families_data_download() (in module common_reports_api.tests.test_common_reports_api) test_families_data_download_no_permissions() (in module common_reports_api.tests.test_common_reports_api) test_families_tags_download() (in module common_reports_api.tests.test_common_reports_api) test_families_tags_download_errors_on_bad_body() (in module common_reports_api.tests.test_common_reports_api) test_family_api_permissions() (in module family_api.tests.test_family_api) test_family_counters() (in module common_reports_api.tests.test_common_reports_api) test_family_counters_download() (in module common_reports_api.tests.test_common_reports_api) test_family_details_view() (in module family_api.tests.test_family_api) test_family_details_view_nonexistent() (in module family_api.tests.test_family_api) test_full_family_details_view() (in module family_api.tests.test_family_api) test_full_study_families_view() (in module family_api.tests.test_family_api) test_gene_score_download() (in module gene_scores.tests.test_gene_scores_views) test_gene_scores_list_view() (in module gene_scores.tests.test_gene_scores_views) test_gene_scores_partitions() (in module gene_scores.tests.test_gene_scores_views) (in module gene_scores.tests.test_scores_partitions) test_gene_scores_partitions_bad_request() (in module gene_scores.tests.test_gene_scores_views) test_gene_set_download_missense() (in module gene_sets.tests.test_gene_sets_api) test_gene_sets_collections() (in module gene_sets.tests.test_gene_sets_api) test_gene_sets_empty_query() (in module gene_sets.tests.test_gene_sets_api) test_gene_sets_missing_collection() (in module gene_sets.tests.test_gene_sets_api) test_gene_view_api_permissions() (in module gene_view.tests.test_gene_view) test_gene_view_config() (in module gene_view.tests.test_gene_view) test_gene_view_summary_variants_download() (in module gene_view.tests.test_gene_view) test_gene_view_summary_variants_download_group() (in module gene_view.tests.test_gene_view) test_gene_view_summary_variants_query() (in module gene_view.tests.test_gene_view) test_gene_view_summary_variants_query_group() (in module gene_view.tests.test_gene_view) test_genome_hg19() (in module gpf_instance.tests.test_genome_view) test_genome_hg38() (in module gpf_instance.tests.test_genome_view) test_genome_other() (in module gpf_instance.tests.test_genome_view) test_genotype_browser_download_columns_default() (in module studies.tests.test_study_config_genotype_browser_columns) test_genotype_browser_download_columns_ext() (in module studies.tests.test_study_config_genotype_browser_columns) test_genotype_browser_preview_columns_default() (in module studies.tests.test_study_config_genotype_browser_columns) test_genotype_browser_preview_columns_ext() (in module studies.tests.test_study_config_genotype_browser_columns) test_genotype_data_config_immutability() (in module studies.tests.test_study_wrapper) test_get_bad_gene_set_collection_not_found() (in module gene_sets.tests.test_gene_sets_api) test_get_case_insensitive_gene() (in module genomes_api.tests.test_gene_models_api) test_get_chd8_transcripts() (in module genomes_api.tests.test_gene_models_api) test_get_default_background_model() (in module enrichment_api.tests.test_enrichment_helper_simple) test_get_default_background_model_default() (in module enrichment_api.tests.test_enrichment_helper_simple) test_get_denovo_gene_set_not_found() (in module gene_sets.tests.test_gene_sets_api) test_get_gene_gene_scores_db() (in module gene_scores.tests.test_gene_scores_db) test_get_gene_set_collection_empty_query() (in module gene_sets.tests.test_gene_sets_api) test_get_gene_set_download_synonymous_autism() (in module gene_sets.tests.test_gene_sets_api) test_get_gene_set_download_synonymous_recurrent() (in module gene_sets.tests.test_gene_sets_api) test_get_gene_set_download_synonymous_triple() (in module gene_sets.tests.test_gene_sets_api) test_get_gene_symbols() (in module gene_profiles_api.tests.test_agp_api) test_get_genes_by_score() (in module gene_scores.tests.test_gene_scores) test_get_genomic_scores() (in module genomic_scores_api.tests.test_genomic_scores_api) test_get_gpf_version() (in module gpf_instance.tests.test_version_api) test_get_links() (in module gene_profiles_api.tests.test_agp_api) test_get_main_gene_set_not_found() (in module gene_sets.tests.test_gene_sets_api) test_get_nonexistant_gene_transcripts() (in module genomes_api.tests.test_gene_models_api) test_get_person_sets_collection_stats() (in module person_sets_api.tests.test_person_sets_api) test_get_person_sets_collection_stats_no_id() (in module person_sets_api.tests.test_person_sets_api) test_get_person_sets_collection_stats_nonexistent() (in module person_sets_api.tests.test_person_sets_api) test_get_selected_counting_models() (in module enrichment_api.tests.test_enrichment_helper_simple) test_get_selected_counting_models_default() (in module enrichment_api.tests.test_enrichment_helper_simple) test_get_selected_counting_models_default_with_counting() (in module enrichment_api.tests.test_enrichment_helper_simple) test_get_selected_person_set_collections() (in module enrichment_api.tests.test_enrichment_helper_simple) test_get_selected_person_set_collections_default() (in module enrichment_api.tests.test_enrichment_helper_simple) test_get_statistic() (in module gene_profiles_api.tests.test_agp_api) test_get_statistics() (in module gene_profiles_api.tests.test_agp_api) test_get_study_background() (in module enrichment_api.tests.test_enrichment_helper_simple) test_get_study_enrichment_config() (in module enrichment_api.tests.test_enrichment_helper_simple) test_get_t4c8_score() (in module gene_scores.tests.test_gene_scores) test_gpf_about_description() (in module gpf_instance.tests.test_version_api) test_gpf_fixture() (in module enrichment_api.tests.test_enrichment_helper_simple) test_gpf_main_description() (in module gpf_instance.tests.test_version_api) test_histograms_beta() (in module measures_api.tests.test_measures_api) test_inheritance_type_column() (in module studies.tests.test_response_transformer_columns) test_is_denovo() (in module studies.tests.test_response_transformer_columns) test_is_group_dataset() (in module studies.tests.test_study_wrapper) test_is_group_study() (in module studies.tests.test_study_wrapper) test_list_families_view() (in module family_api.tests.test_family_api) test_list_families_view_nonexistent() (in module family_api.tests.test_family_api) test_list_families_view_tag_filter() (in module family_api.tests.test_family_api) test_list_families_view_tag_filter_multiple() (in module family_api.tests.test_family_api) test_list_members_view() (in module family_api.tests.test_family_api) test_list_members_view_nonexistent() (in module family_api.tests.test_family_api) test_list_tags_view() (in module family_api.tests.test_family_api) test_main_gene_set_not_found() (in module gene_sets.tests.test_gene_sets_api) test_make_config() (in module studies.tests.test_study_wrapper) test_measures_api_permissions() (in module measures_api.tests.test_measures_api) test_measures_list_categorical() (in module measures_api.tests.test_measures_api) test_measures_list_continuous() (in module measures_api.tests.test_measures_api) test_measures_list_wrong_request() (in module measures_api.tests.test_measures_api) test_member_details_view() (in module family_api.tests.test_family_api) test_member_details_view_nonexistent() (in module family_api.tests.test_family_api) test_nested_queries() (in module studies.tests.test_study_wrapper_queries) test_person_set_collection_queries() (in module studies.tests.test_study_wrapper_person_sets) test_pheno_measure_genotype_browser_columns() (in module studies.tests.test_pheno_measures_columns)

test_pheno_tool_api_permissions() (in module pheno_tool_api.tests.test_pheno_tool_api) test_pheno_tool_download_valid_request() (in module pheno_tool_api.tests.test_pheno_tool_api) test_pheno_tool_view_cnv_on_non_cnv_study() (in module pheno_tool_api.tests.test_pheno_tool_api) test_pheno_tool_view_family_ids_filter() (in module pheno_tool_api.tests.test_pheno_tool_api) test_pheno_tool_view_missense() (in module pheno_tool_api.tests.test_pheno_tool_api) test_pheno_tool_view_missing_dataset() (in module pheno_tool_api.tests.test_pheno_tool_api) test_pheno_tool_view_missing_measure() (in module pheno_tool_api.tests.test_pheno_tool_api) test_pheno_tool_view_na_values() (in module pheno_tool_api.tests.test_pheno_tool_api) test_pheno_tool_view_normalize() (in module pheno_tool_api.tests.test_pheno_tool_api) test_pheno_tool_view_pheno_filter() (in module pheno_tool_api.tests.test_pheno_tool_api) test_pheno_tool_view_query_no_limit() (in module pheno_tool_api.tests.test_pheno_tool_api) test_pheno_tool_view_valid_request() (in module pheno_tool_api.tests.test_pheno_tool_api) test_phenotype_attr_columns() (in module studies.tests.test_response_transformer_columns) test_query_affected_status() (in module studies.tests.test_study_wrapper_queries) test_query_all_variants() (in module studies.tests.test_study_wrapper_queries) test_query_complex_query() (in module studies.tests.test_study_wrapper_queries) test_query_effect_types_variants() (in module studies.tests.test_study_wrapper_queries) test_query_family_filters() (in module studies.tests.test_study_wrapper_queries) test_query_family_variants() (in module studies.tests.test_study_wrapper_queries) test_query_gene_scores() (in module studies.tests.test_study_wrapper_queries) test_query_gene_scores_formatting() (in module studies.tests.test_study_wrapper_queries) test_query_gene_view_summary_variants_dataset() (in module gene_view.tests.test_gene_view) test_query_gene_view_summary_variants_download_dataset() (in module gene_view.tests.test_gene_view) test_query_gene_view_summary_variants_download_study() (in module gene_view.tests.test_gene_view) test_query_gene_view_summary_variants_study() (in module gene_view.tests.test_gene_view) test_query_inheritance_types() (in module studies.tests.test_study_wrapper_queries) test_query_limit_variants() (in module studies.tests.test_study_wrapper_queries) test_query_person_filters() (in module studies.tests.test_study_wrapper_queries) test_query_present_in_child() (in module studies.tests.test_study_wrapper_queries) test_query_present_in_parent() (in module studies.tests.test_study_wrapper_queries) test_query_present_in_parent_and_present_in_child() (in module studies.tests.test_study_wrapper_queries) test_query_present_in_parent_and_present_in_child_and_phenotypes() (in module studies.tests.test_study_wrapper_queries) test_query_preview_have_pheno_column_values() (in module genotype_browser.tests.test_pheno_columns) test_query_regions_variants() (in module studies.tests.test_study_wrapper_queries) test_query_request_simple() (in module studies.tests.test_study_query_request) test_query_sexes_variants() (in module studies.tests.test_study_wrapper_queries) test_query_study_filters() (in module studies.tests.test_study_wrapper_queries) test_query_unique_family_variants() (in module studies.tests.test_study_wrapper_queries) test_query_variant_type_variants() (in module studies.tests.test_study_wrapper_queries) test_query_with_pheno_filters() (in module genotype_browser.tests.test_pheno_filters) test_regressions() (in module measures_api.tests.test_measures_api) test_role_list() (in module measures_api.tests.test_measures_api) test_scores_created() (in module gene_scores.tests.test_gene_scores) test_search_gene_symbols() (in module genomes_api.tests.test_gene_models_api) test_sentry_invalid_cookie() (in module sentry.tests.test_sentry) test_sentry_missing_cookie() (in module sentry.tests.test_sentry) test_sentry_missing_env() (in module sentry.tests.test_sentry) test_sentry_valid_cookie() (in module sentry.tests.test_sentry) test_serialize() (in module enrichment_api.tests.test_enrichment_serializer) test_serialize_enrichment_result() (in module enrichment_api.tests.test_enrichment_serializer) test_special_attr_columns() (in module studies.tests.test_response_transformer_columns) test_special_attrs_formatting() (in module studies.tests.test_response_transformer_columns) test_study_1() (in module enrichment_api.tests.test_t4c8_enrichment) test_study_1_enrichment() (in module enrichment_api.tests.test_t4c8_enrichment) test_study_1_enrichment_with_caching() (in module enrichment_api.tests.test_t4c8_enrichment) test_study_2_query_inheritance_variants() (in module studies.tests.test_study_wrapper_queries) test_study_with_phenotype_data() (in module studies.tests.test_pheno_measures_columns) test_study_wrapper_download_columns_ext() (in module studies.tests.test_study_config_genotype_browser_columns) test_study_wrapper_preview_columns_ext() (in module studies.tests.test_study_config_genotype_browser_columns) test_summary_variant_ids() (in module studies.tests.test_study_wrapper_unique_variants_query) test_t4c8_coding_len_background() (in module enrichment_api.tests.test_t4c8_enrichment) test_t4c8_dataset() (in module studies.tests.test_study_wrapper) test_t4c8_score_available() (in module gene_scores.tests.test_gene_scores) test_t4c8_setup() (in module enrichment_api.tests.test_t4c8_enrichment) test_t4c8_study_1() (in module studies.tests.test_study_wrapper) test_t4c8_study_2() (in module studies.tests.test_study_wrapper) test_transform_and_mode_family_tags_kwargs() (in module studies.tests.test_query_transformer_family_tags) test_transform_complex_family_tags_kwargs() (in module studies.tests.test_query_transformer_family_tags) test_transform_deselected_family_tags_kwargs() (in module studies.tests.test_query_transformer_family_tags) test_transform_or_mode_family_tags_kwargs() (in module studies.tests.test_query_transformer_family_tags) test_transform_parent_zygosity_with_neither() (in module studies.tests.test_query_transformer_present_in_child_and_parent) test_transform_present_in_child_and_present_in_parent() (in module studies.tests.test_query_transformer_present_in_child_and_parent) test_transform_present_in_child_and_present_in_parent_inheritance() (in module studies.tests.test_query_transformer_present_in_child_and_parent) test_transform_present_in_child_and_present_in_parent_roles() (in module studies.tests.test_query_transformer_present_in_child_and_parent) test_transform_selected_family_tags_kwargs() (in module studies.tests.test_query_transformer_family_tags) test_unique_family_variants() (in module studies.tests.test_study_wrapper_unique_variants_query) test_update_gpf_about_description_anonymous() (in module gpf_instance.tests.test_version_api) test_update_gpf_main_description_anonymous() (in module gpf_instance.tests.test_version_api) test_validate_gene_symbols() (in module genomes_api.tests.test_gene_models_api) test_variant_reports() (in module common_reports_api.tests.test_common_reports_api) test_variant_reports_full() (in module common_reports_api.tests.test_common_reports_api) test_variant_reports_has_permissions() (in module common_reports_api.tests.test_common_reports_api) test_variant_reports_permissions() (in module common_reports_api.tests.test_common_reports_api) test_zygosity_gender() (in module studies.tests.test_study_wrapper_queries) test_zygosity_roles_children() (in module studies.tests.test_study_wrapper_queries) test_zygosity_roles_parents() (in module studies.tests.test_study_wrapper_queries) test_zygosity_status() (in module studies.tests.test_study_wrapper_queries) TestResult (class in gpf.tools.gpf_validation_runner) TestStatus (class in gpf.tools.gpf_validation_runner) TestSuite (class in gpf.tools.gpf_validation_runner) text (gpf.pheno.common.MeasureType attribute) time_fmt (gpf_web.default_settings.CustomFormatter attribute) to_cshl_full() (gpf.variants.variant.VariantDesc method) to_cshl_short() (gpf.variants.variant.VariantDesc method) to_dict() (gpf.common_reports.common_report.CommonReport method) (gpf.common_reports.denovo_report.DenovoReport method) (gpf.common_reports.denovo_report.DenovoReportTable method) (gpf.common_reports.denovo_report.EffectCell method) (gpf.common_reports.denovo_report.EffectRow method) (gpf.common_reports.family_counter.FamiliesGroupCounters method) (gpf.common_reports.family_counter.FamilyCounter method) (gpf.common_reports.family_report.FamiliesReport method) (gpf.common_reports.people_counter.PeopleCounter method) (gpf.common_reports.people_counter.PeopleCounters method) (gpf.common_reports.people_counter.PeopleReport method) (gpf.parquet.partition_descriptor.PartitionDescriptor method) to_json() (gpf.gene_profile.statistic.GPStatistic method) (gpf.genomic_scores.scores.ScoreDesc method) (gpf.pedigrees.family.Family method) (gpf.pedigrees.family.Person method) (gpf.person_sets.person_sets.PersonSet method) (gpf.person_sets.PersonSet method) (gpf.pheno.pheno_data.Measure method) to_name() (gpf.variants.attributes.Role static method) (gpf.variants.attributes.Sex static method) (gpf.variants.attributes.Status static method) to_pylist() (gpf.parquet.partition_descriptor.Partition method) to_record() (gpf.variants.family_variant.FamilyVariant method) (gpf.variants.variant.SummaryAllele method) (gpf.variants.variant.SummaryVariant method) to_tsv() (gpf.pedigrees.loader.FamiliesLoader static method) to_value() (gpf.variants.attributes.Role static method) (gpf.variants.attributes.Sex static method) (gpf.variants.attributes.Status static method) to_xml_element() (gpf.tools.gpf_validation_runner.TestResult method) (gpf.tools.gpf_validation_runner.TestSuite method) TOMLDict (class in gpf.configuration.study_config_builder) TOMLList (class in gpf.configuration.study_config_builder) tool_id (gpf_instance.extension.GPFTool property) total (gpf.person_sets.ChildrenStats property) (gpf.person_sets.person_sets.ChildrenStats property) transform_attribute_query_to_function() (in module gpf.query_variants.attribute_queries) transform_attribute_query_to_sql_expression() (in module gpf.query_variants.attribute_queries) transform_attribute_query_to_sql_expression_schema1() (in module gpf.query_variants.attribute_queries) transform_cli_args() (in module gpf.pheno.pheno_import) transform_gene_view_summary_variant() (studies.response_transformer.ResponseTransformer method) (studies.study_wrapper.ResponseTransformerProtocol method) transform_gene_view_summary_variant_download() (studies.response_transformer.ResponseTransformer method) (studies.study_wrapper.ResponseTransformerProtocol method) transform_kwargs() (studies.query_transformer.QueryTransformer method) (studies.study_wrapper.QueryTransformerProtocol method) transform_ps_query_to_attribute_queries() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) transform_roles_to_single_role_string() (gpf.query_variants.base_query_variants.QueryVariants static method) translate() (gpf.pedigrees.layout.Layout method) transmission_type (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.variant.SummaryAllele property) (gpf.variants.variant.SummaryVariant property) TransmissionType (class in gpf.variants.attributes) transmitted (gpf.variants.attributes.TransmissionType attribute) TRIO (gpf.pedigrees.family.FamilyTag attribute) trio_study() (in module studies.tests.test_study_config_genotype_browser_columns) trios (gpf.pedigrees.family.Family property) TripleCriteria (class in gpf.gene_sets.denovo_gene_sets_config) try_solve() (gpf.pedigrees.pedigrees.SandwichSolver static method) tvalues (gpf.pheno.utils.lin_regress.LinearRegression property) type (gpf.import_tools.import_tools.Bucket attribute) TYPE_DISPLAY_NAME (gpf.variants.core.Allele attribute)

U

U (gpf.variants.attributes.Sex attribute) ultra_rare() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) unaffected (gpf.variants.attributes.Status attribute) UNAFFECTED_DAD (gpf.pedigrees.family.FamilyTag attribute) UNAFFECTED_MOM (gpf.pedigrees.family.FamilyTag attribute) UNAFFECTED_PRB (gpf.pedigrees.family.FamilyTag attribute) UNAFFECTED_SIB (gpf.pedigrees.family.FamilyTag attribute) undefined (gpf.variants.attributes.Zygosity attribute) unix_timestamp (gpf.pheno.common.ImportManifest attribute) unknown (gpf.variants.attributes.Inheritance attribute) (gpf.variants.attributes.Role attribute) (gpf.variants.attributes.TransmissionType attribute) unregister_genotype_data() (gpf.studies.variants_db.VariantsDb method) unset_tag() (gpf.pedigrees.family.Family method) (gpf.pedigrees.family.Person method) (in module gpf.pedigrees.family_tag_builder) unspecified (gpf.enrichment_tool.event_counters.EnrichmentResult attribute) (gpf.enrichment_tool.event_counters.EventCountersResult attribute) (gpf.enrichment_tool.event_counters.EventsResult attribute) (gpf.enrichment_tool.event_counters.VariantEventsResult attribute) (gpf.person_sets.ChildrenBySex attribute) (gpf.person_sets.ChildrenStats attribute) (gpf.person_sets.person_sets.ChildrenBySex attribute) (gpf.person_sets.person_sets.ChildrenStats attribute) (gpf.variants.attributes.Sex attribute) (gpf.variants.attributes.Status attribute) update_attribute_query_with_compounds() (in module gpf.query_variants.attribute_queries) update_attributes() (gpf.variants.family_variant.FamilyAllele method) (gpf.variants.variant.SummaryAllele method) (gpf.variants.variant.SummaryVariant method) update_cache() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) update_gps_with_values() (gpf.gene_profile.db.GeneProfileDBWriter method) update_study_config() (in module gpf.testing.import_helpers) url_to_pyarrow_fs() (in module gpf.parquet.helpers) use_bit_and_function() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method) (gpf.query_variants.sql.schema2.base_query_builder.Dialect static method) use_ssl (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute) user_queries module user_queries.migrations module user_queries.migrations.0001_initial module users_api module users_api.management module

users_api.management.commands module users_api.management.commands.user_set_name module users_api.management.commands.user_setpasswd module users_api.management.commands.users_remove module users_api.migrations module users_api.migrations.0001_initial module users_api.migrations.0002_auto_20190424_0751 module users_api.migrations.0003_authenticationlog module users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more module users_api.migrations.0005_gpuserstate module users_api.tests module utils module utils.authentication module utils.datasets module utils.email_regex module utils.expand_gene_set module utils.gene_sets module utils.logger module utils.pagination module utils.password_requirements module utils.query_params module utils.streaming_response_util module utils.testing module

V

validate_and_normalize_config() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage class method) (gpf.genotype_storage.genotype_storage.GenotypeStorage class method) (gpf.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage class method) (gpf.parquet_storage.storage.ParquetGenotypeStorage class method) validate_config() (gpf.configuration.gpf_config_parser.GPFConfigParser static method) validate_existing_path() (in module gpf.configuration.utils) validate_path() (in module gpf.configuration.utils) validation_rules (gpf.configuration.gpf_config_parser.GPFConfigValidator attribute) VALIDATION_SCHEMA (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage attribute) (gpf.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage attribute) (gpf.parquet_storage.storage.ParquetGenotypeStorage attribute) value_max_len (gpf.pheno.common.InferenceConfig attribute) value_type (gpf.pheno.common.InferenceConfig attribute) (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) values (gpf.person_sets.person_sets.PersonSetConfig attribute) (gpf.person_sets.PersonSetConfig attribute) values() (gpf.pedigrees.families_data.FamiliesData method) values_domain (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) variant_in_member_fpids (gpf.variants.family_variant.FamilyAllele property) variant_in_members (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) variant_in_roles (gpf.variants.family_variant.FamilyAllele property) variant_in_sexes (gpf.variants.family_variant.FamilyAllele property) variant_in_statuses (gpf.variants.family_variant.FamilyAllele property) variant_to_variant_type() (in module gpf.variants_loaders.raw.flexible_variant_loader) variant_transformer() (studies.response_transformer.ResponseTransformer method) (studies.study_wrapper.ResponseTransformerProtocol method) variant_type (gpf.variants.variant.SummaryAllele property)

variant_types (gpf.variants.variant.SummaryVariant property) VariantDesc (class in gpf.variants.variant) VariantDetails (class in gpf.variants.variant) VariantEvent (class in gpf.enrichment_tool.genotype_helper) VariantEventsResult (class in gpf.enrichment_tool.event_counters) variants_filenames (gpf.variants_loaders.dae.loader.DaeTransmittedLoader property) (gpf.variants_loaders.raw.loader.VariantsLoader property) (gpf.variants_loaders.vcf.loader.VcfLoader property) variants_loader_annotate_and_save() (in module gpf.inmemory_storage.annotation_serialization) variants_loader_load_annotation() (in module gpf.inmemory_storage.annotation_serialization) VariantsDataSerializer (class in gpf.parquet.schema2.serializers) VariantsDb (class in gpf.studies.variants_db) VariantsGenotypesLoader (class in gpf.variants_loaders.raw.loader) VariantsLoader (class in gpf.variants_loaders.raw.loader) VariantsLoaderBatchSource (class in gpf.parquet.schema2.processing_pipeline) VariantsLoaderDecorator (class in gpf.variants_loaders.raw.loader) VariantsLoaderSource (class in gpf.parquet.schema2.processing_pipeline) VariantsParquetWriter (class in gpf.parquet.schema2.variants_parquet_writer) VariantsParquetWriterDeprecated() (in module gpf.parquet.schema2.parquet_io) vcf (gpf.testing.import_helpers.StudyInputLayout attribute) vcf2cshl() (in module gpf.variants.variant) vcf_import() (in module gpf.testing.import_helpers) vcf_liftover_main() (in module gpf.tools.liftover_tools) vcf_study() (in module gpf.testing.import_helpers) VcfFamiliesGenotypes (class in gpf.variants_loaders.vcf.loader) vcffile_chromosomes() (in module gpf.variants_loaders.vcf.loader) VCFLiftoverTool (class in gpf.tools.liftover_tools) VcfLoader (class in gpf.variants_loaders.vcf.loader) VcfSerializer (class in gpf.variants_loaders.vcf.serializer)

W

WDAEAbstractStudy (class in studies.study_wrapper) WDAEConfig (class in gpf_instance.apps) WdaePageNumberPagination (class in utils.pagination) WDAEStudy (class in studies.study_wrapper) WDAEStudyGroup (class in studies.study_wrapper) wgpf_fixture() (in module studies.tests.test_study_group_person_sets_queries) wgpf_instance() (in module studies.tests.test_study_wrapper_person_sets) (in module studies.tests.test_study_wrapper_unique_variants_query) WHERE (gpf.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute) work_dir (gpf.import_tools.import_tools.ImportProject property) (gpf.pheno.common.PhenoImportConfig attribute)

worst_effect (gpf.variants.variant.SummaryAllele property) write() (gpf.parquet.schema2.variants_parquet_writer.VariantsParquetWriter method) write_descriptions() (in module gpf.pheno.pheno_import) write_new_meta() (in module gpf.parquet.schema2.annotate_schema2_parquet) write_reports_to_parquet() (in module gpf.pheno.pheno_import) write_results() (in module gpf.pheno.pheno_import) write_summary_variant() (gpf.parquet.schema2.variants_parquet_writer.VariantsParquetWriter method) write_to_db() (gpf.pheno.common.ImportManifest static method) write_to_parquet() (in module gpf.pheno.pheno_import)

X

x (gpf.pedigrees.layout.Point attribute) X (gpf.variants.attributes.GeneticModel attribute)

X_broken (gpf.variants.attributes.GeneticModel attribute) x_center (gpf.pedigrees.layout.IndividualWithCoordinates property)

Y

y (gpf.pedigrees.layout.Point attribute) y_center (gpf.pedigrees.layout.IndividualWithCoordinates property)

year (gpf.studies.study.GenotypeData property) yellow (gpf_web.default_settings.CustomFormatter attribute)

Z

Zygosity (class in gpf.variants.attributes) zygosity_in_roles (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) zygosity_in_sexes (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property)

zygosity_in_status (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) ZygosityQuery (class in gpf.query_variants.sql.schema2.sql_query_builder)